Job ID = 6626346 SRX = SRX7202520 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 813989 READS because READLEN < 1 Read 16495713 spots for SRR10517642/SRR10517642.sra Written 16495713 spots for SRR10517642/SRR10517642.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626688 ("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 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] 110 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] 5390408 / 15371124 = 0.3507 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 07:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.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 07:41:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:41:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:41:19: 1000000 INFO @ Tue, 14 Jul 2020 07:41:24: 2000000 INFO @ Tue, 14 Jul 2020 07:41:30: 3000000 INFO @ Tue, 14 Jul 2020 07:41:35: 4000000 INFO @ Tue, 14 Jul 2020 07:41:40: 5000000 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 07:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.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 07:41:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:41:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:41:46: 6000000 INFO @ Tue, 14 Jul 2020 07:41:48: 1000000 INFO @ Tue, 14 Jul 2020 07:41:52: 7000000 INFO @ Tue, 14 Jul 2020 07:41:53: 2000000 INFO @ Tue, 14 Jul 2020 07:41:57: 8000000 INFO @ Tue, 14 Jul 2020 07:41:58: 3000000 INFO @ Tue, 14 Jul 2020 07:42:03: 9000000 INFO @ Tue, 14 Jul 2020 07:42:03: 4000000 INFO @ Tue, 14 Jul 2020 07:42:08: 5000000 INFO @ Tue, 14 Jul 2020 07:42:08: 10000000 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 07:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.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 07:42:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:42:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:42:13: 6000000 INFO @ Tue, 14 Jul 2020 07:42:14: 11000000 INFO @ Tue, 14 Jul 2020 07:42:18: 1000000 INFO @ Tue, 14 Jul 2020 07:42:18: 7000000 INFO @ Tue, 14 Jul 2020 07:42:19: 12000000 INFO @ Tue, 14 Jul 2020 07:42:23: 2000000 INFO @ Tue, 14 Jul 2020 07:42:23: 8000000 INFO @ Tue, 14 Jul 2020 07:42:25: 13000000 INFO @ Tue, 14 Jul 2020 07:42:28: 3000000 INFO @ Tue, 14 Jul 2020 07:42:28: 9000000 INFO @ Tue, 14 Jul 2020 07:42:30: 14000000 INFO @ Tue, 14 Jul 2020 07:42:33: 4000000 INFO @ Tue, 14 Jul 2020 07:42:33: 10000000 INFO @ Tue, 14 Jul 2020 07:42:35: 15000000 INFO @ Tue, 14 Jul 2020 07:42:38: 5000000 INFO @ Tue, 14 Jul 2020 07:42:38: 11000000 INFO @ Tue, 14 Jul 2020 07:42:41: 16000000 INFO @ Tue, 14 Jul 2020 07:42:43: 6000000 INFO @ Tue, 14 Jul 2020 07:42:43: 12000000 INFO @ Tue, 14 Jul 2020 07:42:46: 17000000 INFO @ Tue, 14 Jul 2020 07:42:48: 7000000 INFO @ Tue, 14 Jul 2020 07:42:48: 13000000 INFO @ Tue, 14 Jul 2020 07:42:51: 18000000 INFO @ Tue, 14 Jul 2020 07:42:53: 14000000 INFO @ Tue, 14 Jul 2020 07:42:53: 8000000 INFO @ Tue, 14 Jul 2020 07:42:57: 19000000 INFO @ Tue, 14 Jul 2020 07:42:58: 15000000 INFO @ Tue, 14 Jul 2020 07:42:58: 9000000 INFO @ Tue, 14 Jul 2020 07:43:02: 20000000 INFO @ Tue, 14 Jul 2020 07:43:02: 16000000 INFO @ Tue, 14 Jul 2020 07:43:02: 10000000 INFO @ Tue, 14 Jul 2020 07:43:04: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:43:04: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:43:04: #1 total tags in treatment: 8556432 INFO @ Tue, 14 Jul 2020 07:43:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:43:04: #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 07:43:05: #1 tags after filtering in treatment: 7361796 INFO @ Tue, 14 Jul 2020 07:43:05: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 14 Jul 2020 07:43:05: #1 finished! INFO @ Tue, 14 Jul 2020 07:43:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:43:06: #2 number of paired peaks: 5377 INFO @ Tue, 14 Jul 2020 07:43:06: start model_add_line... INFO @ Tue, 14 Jul 2020 07:43:06: start X-correlation... INFO @ Tue, 14 Jul 2020 07:43:06: end of X-cor INFO @ Tue, 14 Jul 2020 07:43:06: #2 finished! INFO @ Tue, 14 Jul 2020 07:43:06: #2 predicted fragment length is 300 bps INFO @ Tue, 14 Jul 2020 07:43:06: #2 alternative fragment length(s) may be 300 bps INFO @ Tue, 14 Jul 2020 07:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.05_model.r INFO @ Tue, 14 Jul 2020 07:43:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:43:07: 17000000 INFO @ Tue, 14 Jul 2020 07:43:07: 11000000 INFO @ Tue, 14 Jul 2020 07:43:12: 18000000 INFO @ Tue, 14 Jul 2020 07:43:12: 12000000 INFO @ Tue, 14 Jul 2020 07:43:16: 19000000 INFO @ Tue, 14 Jul 2020 07:43:17: 13000000 INFO @ Tue, 14 Jul 2020 07:43:21: 20000000 INFO @ Tue, 14 Jul 2020 07:43:22: 14000000 INFO @ Tue, 14 Jul 2020 07:43:23: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:43:23: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:43:23: #1 total tags in treatment: 8556432 INFO @ Tue, 14 Jul 2020 07:43:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:43:23: #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 07:43:24: #1 tags after filtering in treatment: 7361796 INFO @ Tue, 14 Jul 2020 07:43:24: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 14 Jul 2020 07:43:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:43:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:43:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:43:24: #2 number of paired peaks: 5377 INFO @ Tue, 14 Jul 2020 07:43:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:43:25: start X-correlation... INFO @ Tue, 14 Jul 2020 07:43:25: end of X-cor INFO @ Tue, 14 Jul 2020 07:43:25: #2 finished! INFO @ Tue, 14 Jul 2020 07:43:25: #2 predicted fragment length is 300 bps INFO @ Tue, 14 Jul 2020 07:43:25: #2 alternative fragment length(s) may be 300 bps INFO @ Tue, 14 Jul 2020 07:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.10_model.r INFO @ Tue, 14 Jul 2020 07:43:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:43:26: 15000000 INFO @ Tue, 14 Jul 2020 07:43:31: 16000000 INFO @ Tue, 14 Jul 2020 07:43:32: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:43:35: 17000000 INFO @ Tue, 14 Jul 2020 07:43:40: 18000000 INFO @ Tue, 14 Jul 2020 07:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.05_summits.bed INFO @ Tue, 14 Jul 2020 07:43:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5515 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:43:45: 19000000 INFO @ Tue, 14 Jul 2020 07:43:49: 20000000 INFO @ Tue, 14 Jul 2020 07:43:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:43:51: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:43:51: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:43:51: #1 total tags in treatment: 8556432 INFO @ Tue, 14 Jul 2020 07:43:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:43:51: #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 07:43:51: #1 tags after filtering in treatment: 7361796 INFO @ Tue, 14 Jul 2020 07:43:51: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 14 Jul 2020 07:43:51: #1 finished! INFO @ Tue, 14 Jul 2020 07:43:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:43:52: #2 number of paired peaks: 5377 INFO @ Tue, 14 Jul 2020 07:43:52: start model_add_line... INFO @ Tue, 14 Jul 2020 07:43:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:43:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:43:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:43:52: #2 predicted fragment length is 300 bps INFO @ Tue, 14 Jul 2020 07:43:52: #2 alternative fragment length(s) may be 300 bps INFO @ Tue, 14 Jul 2020 07:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.20_model.r INFO @ Tue, 14 Jul 2020 07:43:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:44:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.10_summits.bed INFO @ Tue, 14 Jul 2020 07:44:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4569 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:44:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7202520/SRX7202520.20_summits.bed INFO @ Tue, 14 Jul 2020 07:44:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3363 records, 4 fields): 7 millis CompletedMACS2peakCalling