Job ID = 6626348 SRX = SRX7202523 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 751688 READS because READLEN < 1 Read 14261675 spots for SRR10517644/SRR10517644.sra Written 14261675 spots for SRR10517644/SRR10517644.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626647 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] 142 unmatched pairs [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] 5436462 / 13243281 = 0.4105 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.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, 14 Jul 2020 07:28:11: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:11: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:16: 1000000 INFO @ Tue, 14 Jul 2020 07:28:20: 2000000 INFO @ Tue, 14 Jul 2020 07:28:25: 3000000 INFO @ Tue, 14 Jul 2020 07:28:29: 4000000 INFO @ Tue, 14 Jul 2020 07:28:34: 5000000 INFO @ Tue, 14 Jul 2020 07:28:38: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:28:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.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, 14 Jul 2020 07:28:41: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:41: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:43: 7000000 INFO @ Tue, 14 Jul 2020 07:28:46: 1000000 INFO @ Tue, 14 Jul 2020 07:28:47: 8000000 INFO @ Tue, 14 Jul 2020 07:28:51: 2000000 INFO @ Tue, 14 Jul 2020 07:28:52: 9000000 INFO @ Tue, 14 Jul 2020 07:28:55: 3000000 INFO @ Tue, 14 Jul 2020 07:28:56: 10000000 INFO @ Tue, 14 Jul 2020 07:29:00: 4000000 INFO @ Tue, 14 Jul 2020 07:29:01: 11000000 INFO @ Tue, 14 Jul 2020 07:29:05: 5000000 INFO @ Tue, 14 Jul 2020 07:29:05: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:29:10: 6000000 INFO @ Tue, 14 Jul 2020 07:29:10: 13000000 INFO @ Tue, 14 Jul 2020 07:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.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, 14 Jul 2020 07:29:11: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:11: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:14: 14000000 INFO @ Tue, 14 Jul 2020 07:29:14: 7000000 INFO @ Tue, 14 Jul 2020 07:29:16: 1000000 INFO @ Tue, 14 Jul 2020 07:29:19: 15000000 INFO @ Tue, 14 Jul 2020 07:29:19: 8000000 INFO @ Tue, 14 Jul 2020 07:29:20: 2000000 INFO @ Tue, 14 Jul 2020 07:29:23: 16000000 INFO @ Tue, 14 Jul 2020 07:29:23: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:29:23: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:29:23: #1 total tags in treatment: 6733209 INFO @ Tue, 14 Jul 2020 07:29:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:29:24: #1 tags after filtering in treatment: 6211051 INFO @ Tue, 14 Jul 2020 07:29:24: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:29:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:24: 9000000 INFO @ Tue, 14 Jul 2020 07:29:24: #2 number of paired peaks: 3994 INFO @ Tue, 14 Jul 2020 07:29:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:24: #2 predicted fragment length is 273 bps INFO @ Tue, 14 Jul 2020 07:29:24: #2 alternative fragment length(s) may be 4,273 bps INFO @ Tue, 14 Jul 2020 07:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.05_model.r INFO @ Tue, 14 Jul 2020 07:29:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:25: 3000000 INFO @ Tue, 14 Jul 2020 07:29:29: 10000000 INFO @ Tue, 14 Jul 2020 07:29:30: 4000000 INFO @ Tue, 14 Jul 2020 07:29:33: 11000000 INFO @ Tue, 14 Jul 2020 07:29:36: 5000000 INFO @ Tue, 14 Jul 2020 07:29:38: 12000000 INFO @ Tue, 14 Jul 2020 07:29:41: 6000000 INFO @ Tue, 14 Jul 2020 07:29:42: 13000000 INFO @ Tue, 14 Jul 2020 07:29:43: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:46: 7000000 INFO @ Tue, 14 Jul 2020 07:29:47: 14000000 INFO @ Tue, 14 Jul 2020 07:29:51: 15000000 INFO @ Tue, 14 Jul 2020 07:29:51: 8000000 INFO @ Tue, 14 Jul 2020 07:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.05_summits.bed INFO @ Tue, 14 Jul 2020 07:29:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7274 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:56: 16000000 INFO @ Tue, 14 Jul 2020 07:29:56: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:29:56: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:29:56: #1 total tags in treatment: 6733209 INFO @ Tue, 14 Jul 2020 07:29:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:29:56: #1 tags after filtering in treatment: 6211051 INFO @ Tue, 14 Jul 2020 07:29:56: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:29:56: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:57: 9000000 INFO @ Tue, 14 Jul 2020 07:29:57: #2 number of paired peaks: 3994 INFO @ Tue, 14 Jul 2020 07:29:57: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:57: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:57: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:57: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:57: #2 predicted fragment length is 273 bps INFO @ Tue, 14 Jul 2020 07:29:57: #2 alternative fragment length(s) may be 4,273 bps INFO @ Tue, 14 Jul 2020 07:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.10_model.r INFO @ Tue, 14 Jul 2020 07:29:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:30:02: 10000000 INFO @ Tue, 14 Jul 2020 07:30:07: 11000000 INFO @ Tue, 14 Jul 2020 07:30:12: 12000000 INFO @ Tue, 14 Jul 2020 07:30:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:16: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:30:21: 14000000 INFO @ Tue, 14 Jul 2020 07:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.10_summits.bed INFO @ Tue, 14 Jul 2020 07:30:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5573 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:30:26: 15000000 INFO @ Tue, 14 Jul 2020 07:30:31: 16000000 INFO @ Tue, 14 Jul 2020 07:30:31: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:30:31: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:30:31: #1 total tags in treatment: 6733209 INFO @ Tue, 14 Jul 2020 07:30:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:30:31: #1 tags after filtering in treatment: 6211051 INFO @ Tue, 14 Jul 2020 07:30:31: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:30:31: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:32: #2 number of paired peaks: 3994 INFO @ Tue, 14 Jul 2020 07:30:32: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:32: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:32: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:32: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:32: #2 predicted fragment length is 273 bps INFO @ Tue, 14 Jul 2020 07:30:32: #2 alternative fragment length(s) may be 4,273 bps INFO @ Tue, 14 Jul 2020 07:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.20_model.r INFO @ Tue, 14 Jul 2020 07:30:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:30:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7202523/SRX7202523.20_summits.bed INFO @ Tue, 14 Jul 2020 07:30:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2951 records, 4 fields): 19 millis CompletedMACS2peakCalling