Job ID = 6367698 SRX = SRX395522 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:05 prefetch.2.10.7: 1) Downloading 'SRR1054243'... 2020-06-15T23:34:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:51 prefetch.2.10.7: 'SRR1054243' is valid 2020-06-15T23:34:51 prefetch.2.10.7: 1) 'SRR1054243' was downloaded successfully Read 6869833 spots for SRR1054243/SRR1054243.sra Written 6869833 spots for SRR1054243/SRR1054243.sra 2020-06-15T23:35:20 prefetch.2.10.7: 1) Downloading 'SRR1054244'... 2020-06-15T23:35:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:03 prefetch.2.10.7: 'SRR1054244' is valid 2020-06-15T23:36:03 prefetch.2.10.7: 1) 'SRR1054244' was downloaded successfully Read 4751315 spots for SRR1054244/SRR1054244.sra Written 4751315 spots for SRR1054244/SRR1054244.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:49 11621148 reads; of these: 11621148 (100.00%) were unpaired; of these: 240935 (2.07%) aligned 0 times 9526040 (81.97%) aligned exactly 1 time 1854173 (15.96%) aligned >1 times 97.93% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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_rmdupse_core] 1312489 / 11380213 = 0.1153 in library ' ' 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, 16 Jun 2020 08:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.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, 16 Jun 2020 08:40:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:47: 1000000 INFO @ Tue, 16 Jun 2020 08:40:53: 2000000 INFO @ Tue, 16 Jun 2020 08:41:00: 3000000 INFO @ Tue, 16 Jun 2020 08:41:06: 4000000 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, 16 Jun 2020 08:41:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.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, 16 Jun 2020 08:41:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:13: 5000000 INFO @ Tue, 16 Jun 2020 08:41:18: 1000000 INFO @ Tue, 16 Jun 2020 08:41:20: 6000000 INFO @ Tue, 16 Jun 2020 08:41:25: 2000000 INFO @ Tue, 16 Jun 2020 08:41:27: 7000000 INFO @ Tue, 16 Jun 2020 08:41:32: 3000000 INFO @ Tue, 16 Jun 2020 08:41:35: 8000000 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, 16 Jun 2020 08:41:39: 4000000 INFO @ Tue, 16 Jun 2020 08:41:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.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, 16 Jun 2020 08:41:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:42: 9000000 INFO @ Tue, 16 Jun 2020 08:41:46: 5000000 INFO @ Tue, 16 Jun 2020 08:41:48: 1000000 INFO @ Tue, 16 Jun 2020 08:41:49: 10000000 INFO @ Tue, 16 Jun 2020 08:41:50: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:50: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:50: #1 total tags in treatment: 10067724 INFO @ Tue, 16 Jun 2020 08:41:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:41:50: #1 tags after filtering in treatment: 10067724 INFO @ Tue, 16 Jun 2020 08:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:51: #2 number of paired peaks: 346 WARNING @ Tue, 16 Jun 2020 08:41:51: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:51: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:41:51: #2 alternative fragment length(s) may be 2,27,567,569 bps INFO @ Tue, 16 Jun 2020 08:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:51: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:51: #2 You may need to consider one of the other alternative d(s): 2,27,567,569 WARNING @ Tue, 16 Jun 2020 08:41:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:41:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:54: 6000000 INFO @ Tue, 16 Jun 2020 08:41:55: 2000000 INFO @ Tue, 16 Jun 2020 08:42:01: 7000000 INFO @ Tue, 16 Jun 2020 08:42:03: 3000000 INFO @ Tue, 16 Jun 2020 08:42:08: 8000000 INFO @ Tue, 16 Jun 2020 08:42:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:10: 4000000 INFO @ Tue, 16 Jun 2020 08:42:15: 9000000 INFO @ Tue, 16 Jun 2020 08:42:17: 5000000 INFO @ Tue, 16 Jun 2020 08:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:22: 10000000 INFO @ Tue, 16 Jun 2020 08:42:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:23: #1 total tags in treatment: 10067724 INFO @ Tue, 16 Jun 2020 08:42:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:42:23: #1 tags after filtering in treatment: 10067724 INFO @ Tue, 16 Jun 2020 08:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:24: #2 number of paired peaks: 346 WARNING @ Tue, 16 Jun 2020 08:42:24: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:24: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:42:24: #2 alternative fragment length(s) may be 2,27,567,569 bps INFO @ Tue, 16 Jun 2020 08:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.10_model.r WARNING @ Tue, 16 Jun 2020 08:42:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:24: #2 You may need to consider one of the other alternative d(s): 2,27,567,569 WARNING @ Tue, 16 Jun 2020 08:42:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:42:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:25: 6000000 INFO @ Tue, 16 Jun 2020 08:42:31: 7000000 INFO @ Tue, 16 Jun 2020 08:42:38: 8000000 INFO @ Tue, 16 Jun 2020 08:42:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:45: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:42:51: 10000000 INFO @ Tue, 16 Jun 2020 08:42:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:52: #1 total tags in treatment: 10067724 INFO @ Tue, 16 Jun 2020 08:42:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:42:52: #1 tags after filtering in treatment: 10067724 INFO @ Tue, 16 Jun 2020 08:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:53: #2 number of paired peaks: 346 WARNING @ Tue, 16 Jun 2020 08:42:53: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:53: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:42:53: #2 alternative fragment length(s) may be 2,27,567,569 bps INFO @ Tue, 16 Jun 2020 08:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:53: #2 You may need to consider one of the other alternative d(s): 2,27,567,569 WARNING @ Tue, 16 Jun 2020 08:42:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:42:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395522/SRX395522.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:22: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling