Job ID = 6367041 SRX = SRX2761386 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:53 prefetch.2.10.7: 1) Downloading 'SRR5476960'... 2020-06-15T23:04:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:32 prefetch.2.10.7: 1) 'SRR5476960' was downloaded successfully Read 17765196 spots for SRR5476960/SRR5476960.sra Written 17765196 spots for SRR5476960/SRR5476960.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: 00:04:17 17765196 reads; of these: 17765196 (100.00%) were unpaired; of these: 851238 (4.79%) aligned 0 times 12668254 (71.31%) aligned exactly 1 time 4245704 (23.90%) aligned >1 times 95.21% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 2295466 / 16913958 = 0.1357 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 08:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.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 08:16:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:14: 1000000 INFO @ Tue, 16 Jun 2020 08:16:19: 2000000 INFO @ Tue, 16 Jun 2020 08:16:24: 3000000 INFO @ Tue, 16 Jun 2020 08:16:28: 4000000 INFO @ Tue, 16 Jun 2020 08:16:33: 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, 16 Jun 2020 08:16:38: 6000000 INFO @ Tue, 16 Jun 2020 08:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.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 08:16:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:43: 7000000 INFO @ Tue, 16 Jun 2020 08:16:44: 1000000 INFO @ Tue, 16 Jun 2020 08:16:48: 8000000 INFO @ Tue, 16 Jun 2020 08:16:50: 2000000 INFO @ Tue, 16 Jun 2020 08:16:53: 9000000 INFO @ Tue, 16 Jun 2020 08:16:55: 3000000 INFO @ Tue, 16 Jun 2020 08:16:57: 10000000 INFO @ Tue, 16 Jun 2020 08:17:01: 4000000 INFO @ Tue, 16 Jun 2020 08:17:02: 11000000 INFO @ Tue, 16 Jun 2020 08:17:07: 5000000 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 08:17:07: 12000000 INFO @ Tue, 16 Jun 2020 08:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.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 08:17:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:12: 13000000 INFO @ Tue, 16 Jun 2020 08:17:12: 6000000 INFO @ Tue, 16 Jun 2020 08:17:15: 1000000 INFO @ Tue, 16 Jun 2020 08:17:17: 14000000 INFO @ Tue, 16 Jun 2020 08:17:18: 7000000 INFO @ Tue, 16 Jun 2020 08:17:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:20: #1 total tags in treatment: 14618492 INFO @ Tue, 16 Jun 2020 08:17:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:20: #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 08:17:20: #1 tags after filtering in treatment: 14618492 INFO @ Tue, 16 Jun 2020 08:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:21: 2000000 INFO @ Tue, 16 Jun 2020 08:17:21: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 08:17:21: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:17:21: #2 alternative fragment length(s) may be 1,36,596 bps INFO @ Tue, 16 Jun 2020 08:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.05_model.r WARNING @ Tue, 16 Jun 2020 08:17:21: #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 08:17:21: #2 You may need to consider one of the other alternative d(s): 1,36,596 WARNING @ Tue, 16 Jun 2020 08:17:21: #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 08:17:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:24: 8000000 INFO @ Tue, 16 Jun 2020 08:17:27: 3000000 INFO @ Tue, 16 Jun 2020 08:17:30: 9000000 INFO @ Tue, 16 Jun 2020 08:17:33: 4000000 INFO @ Tue, 16 Jun 2020 08:17:36: 10000000 INFO @ Tue, 16 Jun 2020 08:17:39: 5000000 INFO @ Tue, 16 Jun 2020 08:17:42: 11000000 INFO @ Tue, 16 Jun 2020 08:17:45: 6000000 INFO @ Tue, 16 Jun 2020 08:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:48: 12000000 INFO @ Tue, 16 Jun 2020 08:17:50: 7000000 INFO @ Tue, 16 Jun 2020 08:17:53: 13000000 INFO @ Tue, 16 Jun 2020 08:17:56: 8000000 INFO @ Tue, 16 Jun 2020 08:17:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:59: 14000000 INFO @ Tue, 16 Jun 2020 08:18:01: 9000000 INFO @ Tue, 16 Jun 2020 08:18:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:03: #1 total tags in treatment: 14618492 INFO @ Tue, 16 Jun 2020 08:18:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:03: #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 08:18:03: #1 tags after filtering in treatment: 14618492 INFO @ Tue, 16 Jun 2020 08:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:04: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 08:18:04: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:04: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:18:04: #2 alternative fragment length(s) may be 1,36,596 bps INFO @ Tue, 16 Jun 2020 08:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:04: #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 08:18:04: #2 You may need to consider one of the other alternative d(s): 1,36,596 WARNING @ Tue, 16 Jun 2020 08:18:04: #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 08:18:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:07: 10000000 INFO @ Tue, 16 Jun 2020 08:18:12: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:18:17: 12000000 INFO @ Tue, 16 Jun 2020 08:18:23: 13000000 INFO @ Tue, 16 Jun 2020 08:18:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:28: 14000000 INFO @ Tue, 16 Jun 2020 08:18:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:32: #1 total tags in treatment: 14618492 INFO @ Tue, 16 Jun 2020 08:18:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:32: #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 08:18:32: #1 tags after filtering in treatment: 14618492 INFO @ Tue, 16 Jun 2020 08:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:33: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 08:18:33: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:18:33: #2 alternative fragment length(s) may be 1,36,596 bps INFO @ Tue, 16 Jun 2020 08:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.20_model.r WARNING @ Tue, 16 Jun 2020 08:18:33: #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 08:18:33: #2 You may need to consider one of the other alternative d(s): 1,36,596 WARNING @ Tue, 16 Jun 2020 08:18:33: #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 08:18:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761386/SRX2761386.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling