Job ID = 6497411 SRX = SRX494823 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:34:19 prefetch.2.10.7: 1) Downloading 'SRR1198355'... 2020-06-25T22:34:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:38:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:38:31 prefetch.2.10.7: 1) 'SRR1198355' was downloaded successfully Read 16505446 spots for SRR1198355/SRR1198355.sra Written 16505446 spots for SRR1198355/SRR1198355.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: 00:00:01 Multiseed full-index search: 00:02:56 16505446 reads; of these: 16505446 (100.00%) were unpaired; of these: 4910900 (29.75%) aligned 0 times 9423630 (57.09%) aligned exactly 1 time 2170916 (13.15%) aligned >1 times 70.25% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 1085875 / 11594546 = 0.0937 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 @ Fri, 26 Jun 2020 07:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.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 @ Fri, 26 Jun 2020 07:46:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:46:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:46:39: 1000000 INFO @ Fri, 26 Jun 2020 07:46:46: 2000000 INFO @ Fri, 26 Jun 2020 07:46:54: 3000000 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 @ Fri, 26 Jun 2020 07:47:01: 4000000 INFO @ Fri, 26 Jun 2020 07:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.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 @ Fri, 26 Jun 2020 07:47:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:47:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:47:08: 5000000 INFO @ Fri, 26 Jun 2020 07:47:09: 1000000 INFO @ Fri, 26 Jun 2020 07:47:16: 6000000 INFO @ Fri, 26 Jun 2020 07:47:17: 2000000 INFO @ Fri, 26 Jun 2020 07:47:24: 7000000 INFO @ Fri, 26 Jun 2020 07:47:25: 3000000 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 @ Fri, 26 Jun 2020 07:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.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 @ Fri, 26 Jun 2020 07:47:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:47:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:47:32: 8000000 INFO @ Fri, 26 Jun 2020 07:47:33: 4000000 INFO @ Fri, 26 Jun 2020 07:47:39: 1000000 INFO @ Fri, 26 Jun 2020 07:47:40: 9000000 INFO @ Fri, 26 Jun 2020 07:47:40: 5000000 INFO @ Fri, 26 Jun 2020 07:47:47: 2000000 INFO @ Fri, 26 Jun 2020 07:47:48: 6000000 INFO @ Fri, 26 Jun 2020 07:47:48: 10000000 INFO @ Fri, 26 Jun 2020 07:47:52: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:47:52: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:47:52: #1 total tags in treatment: 10508671 INFO @ Fri, 26 Jun 2020 07:47:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:47:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:47:52: #1 tags after filtering in treatment: 10508671 INFO @ Fri, 26 Jun 2020 07:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:47:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:47:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:47:53: #2 number of paired peaks: 305 WARNING @ Fri, 26 Jun 2020 07:47:53: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Fri, 26 Jun 2020 07:47:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:47:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:47:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:47:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:47:53: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:47:53: #2 alternative fragment length(s) may be 1,33,547,588 bps INFO @ Fri, 26 Jun 2020 07:47:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.05_model.r WARNING @ Fri, 26 Jun 2020 07:47:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:47:53: #2 You may need to consider one of the other alternative d(s): 1,33,547,588 WARNING @ Fri, 26 Jun 2020 07:47:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:47:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:55: 3000000 INFO @ Fri, 26 Jun 2020 07:47:55: 7000000 INFO @ Fri, 26 Jun 2020 07:48:03: 4000000 INFO @ Fri, 26 Jun 2020 07:48:03: 8000000 INFO @ Fri, 26 Jun 2020 07:48:10: 5000000 INFO @ Fri, 26 Jun 2020 07:48:11: 9000000 INFO @ Fri, 26 Jun 2020 07:48:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:48:18: 6000000 INFO @ Fri, 26 Jun 2020 07:48:19: 10000000 INFO @ Fri, 26 Jun 2020 07:48:23: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:48:23: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:48:23: #1 total tags in treatment: 10508671 INFO @ Fri, 26 Jun 2020 07:48:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:48:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:48:23: #1 tags after filtering in treatment: 10508671 INFO @ Fri, 26 Jun 2020 07:48:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:48:23: #1 finished! INFO @ Fri, 26 Jun 2020 07:48:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:48:24: #2 number of paired peaks: 305 WARNING @ Fri, 26 Jun 2020 07:48:24: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Fri, 26 Jun 2020 07:48:24: start model_add_line... INFO @ Fri, 26 Jun 2020 07:48:24: start X-correlation... INFO @ Fri, 26 Jun 2020 07:48:24: end of X-cor INFO @ Fri, 26 Jun 2020 07:48:24: #2 finished! INFO @ Fri, 26 Jun 2020 07:48:24: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:48:24: #2 alternative fragment length(s) may be 1,33,547,588 bps INFO @ Fri, 26 Jun 2020 07:48:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.10_model.r WARNING @ Fri, 26 Jun 2020 07:48:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:48:24: #2 You may need to consider one of the other alternative d(s): 1,33,547,588 WARNING @ Fri, 26 Jun 2020 07:48:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:48:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:48:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:48:25: 7000000 INFO @ Fri, 26 Jun 2020 07:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.05_summits.bed INFO @ Fri, 26 Jun 2020 07:48:26: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:48:33: 8000000 INFO @ Fri, 26 Jun 2020 07:48:40: 9000000 INFO @ Fri, 26 Jun 2020 07:48:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:48:47: 10000000 INFO @ Fri, 26 Jun 2020 07:48:51: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:48:51: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:48:51: #1 total tags in treatment: 10508671 INFO @ Fri, 26 Jun 2020 07:48:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:48:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:48:51: #1 tags after filtering in treatment: 10508671 INFO @ Fri, 26 Jun 2020 07:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:48:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:48:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:48:52: #2 number of paired peaks: 305 WARNING @ Fri, 26 Jun 2020 07:48:52: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Fri, 26 Jun 2020 07:48:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:48:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:48:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:48:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:48:52: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:48:52: #2 alternative fragment length(s) may be 1,33,547,588 bps INFO @ Fri, 26 Jun 2020 07:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.20_model.r WARNING @ Fri, 26 Jun 2020 07:48:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:48:52: #2 You may need to consider one of the other alternative d(s): 1,33,547,588 WARNING @ Fri, 26 Jun 2020 07:48:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:48:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.10_summits.bed INFO @ Fri, 26 Jun 2020 07:48:57: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:49:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494823/SRX494823.20_summits.bed INFO @ Fri, 26 Jun 2020 07:49:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling