Job ID = 6366565 SRX = SRX1936243 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:56 prefetch.2.10.7: 1) Downloading 'SRR3879850'... 2020-06-15T22:51:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:36 prefetch.2.10.7: 1) 'SRR3879850' was downloaded successfully Read 23185843 spots for SRR3879850/SRR3879850.sra Written 23185843 spots for SRR3879850/SRR3879850.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: 00:05:19 23185843 reads; of these: 23185843 (100.00%) were unpaired; of these: 4434353 (19.13%) aligned 0 times 15573328 (67.17%) aligned exactly 1 time 3178162 (13.71%) aligned >1 times 80.87% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 8 files... [bam_rmdupse_core] 2693987 / 18751490 = 0.1437 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 08:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.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 08:05:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:08: 1000000 INFO @ Tue, 16 Jun 2020 08:05:15: 2000000 INFO @ Tue, 16 Jun 2020 08:05:22: 3000000 INFO @ Tue, 16 Jun 2020 08:05:29: 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 08:05:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.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 08:05:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:36: 5000000 INFO @ Tue, 16 Jun 2020 08:05:38: 1000000 INFO @ Tue, 16 Jun 2020 08:05:44: 6000000 INFO @ Tue, 16 Jun 2020 08:05:45: 2000000 INFO @ Tue, 16 Jun 2020 08:05:51: 7000000 INFO @ Tue, 16 Jun 2020 08:05:52: 3000000 INFO @ Tue, 16 Jun 2020 08:05:58: 8000000 INFO @ Tue, 16 Jun 2020 08:05:59: 4000000 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 08:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.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 08:06:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:05: 9000000 INFO @ Tue, 16 Jun 2020 08:06:06: 5000000 INFO @ Tue, 16 Jun 2020 08:06:08: 1000000 INFO @ Tue, 16 Jun 2020 08:06:13: 10000000 INFO @ Tue, 16 Jun 2020 08:06:13: 6000000 INFO @ Tue, 16 Jun 2020 08:06:15: 2000000 INFO @ Tue, 16 Jun 2020 08:06:20: 7000000 INFO @ Tue, 16 Jun 2020 08:06:20: 11000000 INFO @ Tue, 16 Jun 2020 08:06:22: 3000000 INFO @ Tue, 16 Jun 2020 08:06:27: 8000000 INFO @ Tue, 16 Jun 2020 08:06:27: 12000000 INFO @ Tue, 16 Jun 2020 08:06:29: 4000000 INFO @ Tue, 16 Jun 2020 08:06:34: 9000000 INFO @ Tue, 16 Jun 2020 08:06:34: 13000000 INFO @ Tue, 16 Jun 2020 08:06:36: 5000000 INFO @ Tue, 16 Jun 2020 08:06:41: 10000000 INFO @ Tue, 16 Jun 2020 08:06:41: 14000000 INFO @ Tue, 16 Jun 2020 08:06:43: 6000000 INFO @ Tue, 16 Jun 2020 08:06:48: 15000000 INFO @ Tue, 16 Jun 2020 08:06:48: 11000000 INFO @ Tue, 16 Jun 2020 08:06:50: 7000000 INFO @ Tue, 16 Jun 2020 08:06:55: 16000000 INFO @ Tue, 16 Jun 2020 08:06:55: 12000000 INFO @ Tue, 16 Jun 2020 08:06:55: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:06:55: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:06:55: #1 total tags in treatment: 16057503 INFO @ Tue, 16 Jun 2020 08:06:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:55: #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 08:06:55: #1 tags after filtering in treatment: 16057503 INFO @ Tue, 16 Jun 2020 08:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:57: #2 number of paired peaks: 272 WARNING @ Tue, 16 Jun 2020 08:06:57: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:57: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:57: #2 alternative fragment length(s) may be 1,11,50,478,553,585 bps INFO @ Tue, 16 Jun 2020 08:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:57: #2 You may need to consider one of the other alternative d(s): 1,11,50,478,553,585 WARNING @ Tue, 16 Jun 2020 08:06:57: #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 08:06:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:57: 8000000 INFO @ Tue, 16 Jun 2020 08:07:02: 13000000 INFO @ Tue, 16 Jun 2020 08:07:04: 9000000 INFO @ Tue, 16 Jun 2020 08:07:09: 14000000 INFO @ Tue, 16 Jun 2020 08:07:11: 10000000 INFO @ Tue, 16 Jun 2020 08:07:15: 15000000 INFO @ Tue, 16 Jun 2020 08:07:17: 11000000 INFO @ Tue, 16 Jun 2020 08:07:22: 16000000 INFO @ Tue, 16 Jun 2020 08:07:22: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:07:22: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:07:22: #1 total tags in treatment: 16057503 INFO @ Tue, 16 Jun 2020 08:07:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:22: #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 08:07:23: #1 tags after filtering in treatment: 16057503 INFO @ Tue, 16 Jun 2020 08:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:24: #2 number of paired peaks: 272 WARNING @ Tue, 16 Jun 2020 08:07:24: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:24: 12000000 INFO @ Tue, 16 Jun 2020 08:07:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:07:24: #2 alternative fragment length(s) may be 1,11,50,478,553,585 bps INFO @ Tue, 16 Jun 2020 08:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.10_model.r WARNING @ Tue, 16 Jun 2020 08:07:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:24: #2 You may need to consider one of the other alternative d(s): 1,11,50,478,553,585 WARNING @ Tue, 16 Jun 2020 08:07:24: #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 08:07:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:30: 13000000 INFO @ Tue, 16 Jun 2020 08:07:36: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:42: 15000000 INFO @ Tue, 16 Jun 2020 08:07:48: 16000000 INFO @ Tue, 16 Jun 2020 08:07:49: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:07:49: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:07:49: #1 total tags in treatment: 16057503 INFO @ Tue, 16 Jun 2020 08:07:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:49: #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 08:07:49: #1 tags after filtering in treatment: 16057503 INFO @ Tue, 16 Jun 2020 08:07:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:50: #2 number of paired peaks: 272 WARNING @ Tue, 16 Jun 2020 08:07:50: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:50: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:07:50: #2 alternative fragment length(s) may be 1,11,50,478,553,585 bps INFO @ Tue, 16 Jun 2020 08:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:50: #2 You may need to consider one of the other alternative d(s): 1,11,50,478,553,585 WARNING @ Tue, 16 Jun 2020 08:07:50: #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 08:07:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936243/SRX1936243.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:34: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling