[ERROR] No full-alignment output for file (Illumina)

[dgslos]

Hi,

I'm using the Clair3-Illumina conda package on haploid data and I'm getting these "[ERROR] No full-alignment output for file" errors. Something related to clair3 or my data?

[INFO] CLAIR3 VERSION: v1.0.6
[INFO] BAM FILE PATH: /home/genomics/dslos/06_development/fusarium/01_mapping/./MY0231.BWA.bam
[INFO] REFERENCE FILE PATH: /home/genomics/dslos/06_development/fusarium/ref/polished.fasta
[INFO] MODEL PATH: /opt/miniforge3/envs/clair3-illumina/bin/models/ilmn
[INFO] OUTPUT FOLDER: /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231
[INFO] PLATFORM: ilmn
[INFO] THREADS: 20
[INFO] BED FILE PATH: /home/genomics/dslos/06_development/fusarium/02_delineate_c90/final_stack_positions_fusarium_C90.0_SMAP10_CL40_275.bed
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: EMPTY
[INFO] CONDA PREFIX: /opt/miniforge3/envs/clair3-illumina
[INFO] SAMTOOLS PATH: samtools
[INFO] PYTHON PATH: python3
[INFO] PYPY PATH: pypy3
[INFO] PARALLEL PATH: parallel
[INFO] WHATSHAP PATH: whatshap
[INFO] LONGPHASE PATH: EMPTY
[INFO] CHUNK SIZE: 5000000
[INFO] FULL ALIGN PROPORTION: 0.3
[INFO] FULL ALIGN REFERENCE PROPORTION: 0.3
[INFO] PHASING PROPORTION: 0.7
[INFO] MINIMUM MQ: 5
[INFO] MINIMUM COVERAGE: 2
[INFO] SNP AF THRESHOLD: 0.08
[INFO] INDEL AF THRESHOLD: 0.08
[INFO] BASE ERROR IN GVCF: 0.001
[INFO] GQ BIN SIZE IN GVCF: 5
[INFO] ENABLE FILEUP ONLY CALLING: False
[INFO] ENABLE FAST MODE CALLING: False
[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
[INFO] ENABLE PRINTING REFERENCE CALLS: False
[INFO] ENABLE OUTPUT GVCF: False
[INFO] ENABLE HAPLOID PRECISE MODE: False
[INFO] ENABLE HAPLOID SENSITIVE MODE: True
[INFO] ENABLE INCLUDE ALL CTGS CALLING: True
[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: True
[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: False
[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
[INFO] ENABLE LONG INDEL CALLING: False
[INFO] ENABLE C_IMPLEMENT: True

[WARNING] Illumina platform will disable C implement to support short read realignment process!
+ /opt/miniforge3/envs/clair3-illumina/bin/scripts/clair3.sh --bam_fn /home/genomics/dslos/06_development/fusarium/01_mapping/./MY0231.BWA.bam --ref_fn /home/genomics/dslos/06_development/fusarium/ref/polished.fasta --threads 20 --model_path /opt/miniforge3/envs/clair3-illumina/bin/models/ilmn --platform ilmn --output /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231 --bed_fn=/home/genomics/dslos/06_development/fusarium/02_delineate_c90/final_stack_positions_fusarium_C90.0_SMAP10_CL40_275.bed --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=MY0231 --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.3 --ref_pct_full=0.3 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.08 --min_mq=5 --min_coverage=2 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=True --include_all_ctgs=True --no_phasing_for_fa=True --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=False --longphase=EMPTY --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=False --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False

[INFO] Check environment variables
[INFO] --include_all_ctgs enabled
[INFO] Call variant in contigs: contig_50 contig_41 contig_18 contig_42 contig_20 contig_69 contig_12 contig_193 contig_25 contig_16 contig_27 contig_21 contig_49 contig_192 contig_36 contig_90 contig_33 contig_200 contig_194 contig_29 contig_61 contig_161 contig_35 contig_32 contig_190 contig_31
[INFO] Chunk number for each contig: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[INFO] 1/7 Call variants using pileup model
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_192 (chunk 1/1) : 14
Total time elapsed: 2.02 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_50 (chunk 1/1) : 32
Total time elapsed: 2.10 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_193 (chunk 1/1) : 4
Total time elapsed: 2.64 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_36 (chunk 1/1) : 46
Total time elapsed: 2.79 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_16 (chunk 1/1) : 99
Total time elapsed: 3.42 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_42 (chunk 1/1) : 31
Total time elapsed: 2.52 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_20 (chunk 1/1) : 75
Total time elapsed: 2.74 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_49 (chunk 1/1) : 143
Total time elapsed: 4.24 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_90 (chunk 1/1) : 163
Total time elapsed: 5.52 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_18 (chunk 1/1) : 328
Total time elapsed: 8.65 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_69 (chunk 1/1) : 267
Total time elapsed: 8.21 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_12 (chunk 1/1) : 404
Total time elapsed: 9.59 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_200 (chunk 1/1) : 152
Total time elapsed: 4.97 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_41 (chunk 1/1) : 387
Total time elapsed: 8.88 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_21 (chunk 1/1) : 465
Total time elapsed: 16.27 s
[INFO] Delay 1 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_61 (chunk 1/1) : 135
Total time elapsed: 5.16 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_27 (chunk 1/1) : 547
Total time elapsed: 14.39 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_190 (chunk 1/1) : 24
Total time elapsed: 2.64 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_194 (chunk 1/1) : 332
Total time elapsed: 11.39 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_25 (chunk 1/1) : 759
Total time elapsed: 17.16 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_35 (chunk 1/1) : 375
Total time elapsed: 11.41 s
[INFO] Delay 1 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_29 (chunk 1/1) : 363
Total time elapsed: 11.71 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_161 (chunk 1/1) : 285
Total time elapsed: 8.75 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_33 (chunk 1/1) : 458
Total time elapsed: 18.36 s
[INFO] Delay 1 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_32 (chunk 1/1) : 433
Total time elapsed: 13.14 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_31 (chunk 1/1) : 573
Total time elapsed: 12.08 s

real    0m32.658s
user    6m21.829s
sys     0m31.780s
[INFO] 2/7 No phasing for full alignment calling

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 15.0
[INFO] Set reference calls quality cutoff 6.0
[INFO] Low quality reference calls to be processed in contig_20: 2
[INFO] Low quality variants to be processed in contig_20: 21
[INFO] Low quality reference calls to be processed in contig_25: 24
[INFO] Low quality variants to be processed in contig_25: 193
[INFO] Low quality reference calls to be processed in contig_41: 8
[INFO] Low quality variants to be processed in contig_41: 97
[INFO] Low quality reference calls to be processed in contig_18: 13
[INFO] Low quality variants to be processed in contig_18: 107
[WARNING] Cannot find any low-quality 0/0, 0/1 or 1/1 variant in pileup output in contig contig_193
[WARNING] Copying pileup.vcf.gz to /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/merge_output.vcf.gz
[INFO] Low quality reference calls to be processed in contig_193: 0
[INFO] Low quality variants to be processed in contig_193: 0
[INFO] Low quality reference calls to be processed in contig_42: 2
[INFO] Low quality variants to be processed in contig_42: 7
[INFO] Low quality reference calls to be processed in contig_27: 8
[INFO] Low quality variants to be processed in contig_27: 159
[INFO] Low quality reference calls to be processed in contig_49: 3
[INFO] Low quality variants to be processed in contig_49: 39
[INFO] Low quality reference calls to be processed in contig_12: 10
[INFO] Low quality variants to be processed in contig_12: 102
[INFO] Low quality reference calls to be processed in contig_16: 2
[INFO] Low quality variants to be processed in contig_16: 24
[INFO] Low quality reference calls to be processed in contig_21: 13
[INFO] Low quality variants to be processed in contig_21: 128
[INFO] Low quality reference calls to be processed in contig_192: 1
[INFO] Low quality variants to be processed in contig_192: 3
[INFO] Low quality reference calls to be processed in contig_200: 3
[INFO] Low quality variants to be processed in contig_200: 35
[INFO] Low quality reference calls to be processed in contig_33: 5
[INFO] Low quality variants to be processed in contig_33: 139
[INFO] Low quality reference calls to be processed in contig_50: 1
[INFO] Low quality variants to be processed in contig_50: 10
[INFO] Low quality reference calls to be processed in contig_90: 3
[INFO] Low quality variants to be processed in contig_90: 42
[INFO] Low quality reference calls to be processed in contig_29: 8
[INFO] Low quality variants to be processed in contig_29: 87
[INFO] Low quality reference calls to be processed in contig_36: 3
[INFO] Low quality variants to be processed in contig_36: 9
[INFO] Low quality reference calls to be processed in contig_194: 4
[INFO] Low quality variants to be processed in contig_194: 103
[INFO] Low quality reference calls to be processed in contig_69: 6
[INFO] Low quality variants to be processed in contig_69: 78
[INFO] Low quality reference calls to be processed in contig_61: 4
[INFO] Low quality variants to be processed in contig_61: 39
[INFO] Low quality reference calls to be processed in contig_35: 9
[INFO] Low quality variants to be processed in contig_35: 111
[INFO] Low quality reference calls to be processed in contig_161: 8
[INFO] Low quality variants to be processed in contig_161: 71
[INFO] Low quality reference calls to be processed in contig_32: 12
[INFO] Low quality variants to be processed in contig_32: 135
[INFO] Low quality reference calls to be processed in contig_190: 1
[INFO] Low quality variants to be processed in contig_190: 7
[INFO] Low quality reference calls to be processed in contig_31: 18
[INFO] Low quality variants to be processed in contig_31: 145

real    0m0.693s
user    0m4.550s
sys     0m1.888s

[INFO] 6/7 Call low-quality variants using full-alignment model
[INFO] Delay 0 seconds before starting variant calling ...
[WARNING] Skip full-alignment variant calling for empty full-alignment regions
[INFO] Delay 0 seconds before starting variant calling ...
samtools view: writing to standard output failed[mpileup] fail to read the header of -
: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_12 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_12//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_12.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_12.0_1.vcf, remove empty file
[INFO] Delay 0 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_18 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_18//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_18.0_1.vcf
Total time elapsed: 0.20 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_18.0_1.vcf, remove empty file
[INFO] Delay 0 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_29 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_29//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_29.0_1.vcf
Total time elapsed: 1.61 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_29.0_1.vcf, remove empty file
[INFO] Delay 0 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_32 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_32//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_32.0_1.vcf
Total time elapsed: 2.65 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_32.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_200 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_200//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_200.0_1.vcf
Total time elapsed: 2.75 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_200.0_1.vcf, remove empty file
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_192 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_192//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_192.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_192.0_1.vcf, remove empty file
[INFO] Delay 4 seconds before starting variant calling ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_21 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_21//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_21.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_21.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_27 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_27//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_27.0_1.vcf
Total time elapsed: 3.37 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_27.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_31 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_31//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_31.0_1.vcf
Total time elapsed: 4.22 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_31.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_20 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_20//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_20.0_1.vcf
Total time elapsed: 4.51 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_20.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_161 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_161//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_161.0_1.vcf
Total time elapsed: 5.10 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_161.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_42 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_42//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_42.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_42.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_190 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_190//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_190.0_1.vcf
Total time elapsed: 5.91 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_190.0_1.vcf, remove empty file
[INFO] Delay 4 seconds before starting variant calling ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Calling variants ...
Total processed positions in contig_41 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_41//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_41.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_41.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_16 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_16//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_16.0_1.vcf
Total time elapsed: 6.90 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_16.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed[mpileup] fail to read the header of -
: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_194 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_194//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_194.0_1.vcf
Total time elapsed: 7.97 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_194.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed[mpileup] fail to read the header of -
: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_25 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_25//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_25.0_1.vcf
Total time elapsed: 8.58 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_25.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_33 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_33//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_33.0_1.vcf
Total time elapsed: 8.81 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_33.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_35 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_35//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_35.0_1.vcf
Total time elapsed: 7.88 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_35.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_36 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_36//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_36.0_1.vcf
Total time elapsed: 7.69 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_36.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_50 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_50//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_50.0_1.vcf
Total time elapsed: 7.57 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_50.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_49 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_49//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_49.0_1.vcf
Total time elapsed: 7.96 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_49.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_69 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_69//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_69.0_1.vcf
Total time elapsed: 8.35 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_69.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_61 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_61//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_61.0_1.vcf
Total time elapsed: 8.01 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_61.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_90 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_90//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_90.0_1.vcf
Total time elapsed: 8.31 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_90.0_1.vcf, remove empty file

real    0m22.977s
user    1m20.538s
sys     0m16.302s
[WARNING] No vcf file found with prefix:/home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment, output empty vcf file
[WARNING] Copying pileup.vcf.gz to /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/merge_output.vcf.gz
[INFO] Exit in full-alignment variant calling