Job ID = 16432564 SRX = SRX9091661 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 241 READS because READLEN < 1 Read 41986291 spots for SRR12608198/SRR12608198.sra Written 41986291 spots for SRR12608198/SRR12608198.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434972 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Warning: skipping mate #1 of read 'SRR12608198.10399737 10399737 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608198.10399737 10399737 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608198.10399737 10399737 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608198.10399737 10399737 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608198.22423271 22423271 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608198.22423271 22423271 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608198.22423271 22423271 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608198.22423271 22423271 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 33056856 / 33219786 = 0.9951 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 10:29:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:29:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:29:59: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:29:59: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:29:59: #1 total tags in treatment: 166235 INFO @ Tue, 02 Aug 2022 10:29:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:29:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:29:59: #1 tags after filtering in treatment: 140112 INFO @ Tue, 02 Aug 2022 10:29:59: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 10:29:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:29:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:29:59: #2 number of paired peaks: 3344 INFO @ Tue, 02 Aug 2022 10:29:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:29:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:29:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:29:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:29:59: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 10:29:59: #2 alternative fragment length(s) may be 229,251 bps INFO @ Tue, 02 Aug 2022 10:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.05_model.r INFO @ Tue, 02 Aug 2022 10:29:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:29:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:30:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:30:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.05_summits.bed INFO @ Tue, 02 Aug 2022 10:30:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 44 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 10:30:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:26: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:30:26: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:30:26: #1 total tags in treatment: 166235 INFO @ Tue, 02 Aug 2022 10:30:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:30:26: #1 tags after filtering in treatment: 140112 INFO @ Tue, 02 Aug 2022 10:30:26: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 10:30:26: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:26: #2 number of paired peaks: 3344 INFO @ Tue, 02 Aug 2022 10:30:26: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:26: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:26: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:26: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:26: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 10:30:26: #2 alternative fragment length(s) may be 229,251 bps INFO @ Tue, 02 Aug 2022 10:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.10_model.r INFO @ Tue, 02 Aug 2022 10:30:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.10_summits.bed INFO @ Tue, 02 Aug 2022 10:30:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (64 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 10:30:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:53: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:30:58: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:30:58: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:30:58: #1 total tags in treatment: 166235 INFO @ Tue, 02 Aug 2022 10:30:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:30:58: #1 tags after filtering in treatment: 140112 INFO @ Tue, 02 Aug 2022 10:30:58: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 10:30:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:58: #2 number of paired peaks: 3344 INFO @ Tue, 02 Aug 2022 10:30:58: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:58: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:58: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:58: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:58: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 10:30:58: #2 alternative fragment length(s) may be 229,251 bps INFO @ Tue, 02 Aug 2022 10:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.20_model.r INFO @ Tue, 02 Aug 2022 10:30:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091661/SRX9091661.20_summits.bed INFO @ Tue, 02 Aug 2022 10:30:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 95 millis CompletedMACS2peakCalling