Job ID = 6368654 SRX = SRX529214 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:46 prefetch.2.10.7: 1) Downloading 'SRR1265818'... 2020-06-16T00:26:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:50 prefetch.2.10.7: 'SRR1265818' is valid 2020-06-16T00:27:50 prefetch.2.10.7: 1) 'SRR1265818' was downloaded successfully Read 16137366 spots for SRR1265818/SRR1265818.sra Written 16137366 spots for SRR1265818/SRR1265818.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: 00:02:17 16137366 reads; of these: 16137366 (100.00%) were unpaired; of these: 921384 (5.71%) aligned 0 times 12433862 (77.05%) aligned exactly 1 time 2782120 (17.24%) aligned >1 times 94.29% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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_rmdupse_core] 1283707 / 15215982 = 0.0844 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 09:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.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 09:34:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:30: 1000000 INFO @ Tue, 16 Jun 2020 09:34:36: 2000000 INFO @ Tue, 16 Jun 2020 09:34:42: 3000000 INFO @ Tue, 16 Jun 2020 09:34:47: 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 09:34:53: 5000000 INFO @ Tue, 16 Jun 2020 09:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.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 09:34:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:59: 6000000 INFO @ Tue, 16 Jun 2020 09:35:01: 1000000 INFO @ Tue, 16 Jun 2020 09:35:05: 7000000 INFO @ Tue, 16 Jun 2020 09:35:07: 2000000 INFO @ Tue, 16 Jun 2020 09:35:12: 8000000 INFO @ Tue, 16 Jun 2020 09:35:13: 3000000 INFO @ Tue, 16 Jun 2020 09:35:18: 9000000 INFO @ Tue, 16 Jun 2020 09:35:19: 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 09:35:24: 10000000 INFO @ Tue, 16 Jun 2020 09:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.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 09:35:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:25: 5000000 INFO @ Tue, 16 Jun 2020 09:35:31: 1000000 INFO @ Tue, 16 Jun 2020 09:35:31: 11000000 INFO @ Tue, 16 Jun 2020 09:35:31: 6000000 INFO @ Tue, 16 Jun 2020 09:35:36: 2000000 INFO @ Tue, 16 Jun 2020 09:35:37: 12000000 INFO @ Tue, 16 Jun 2020 09:35:38: 7000000 INFO @ Tue, 16 Jun 2020 09:35:42: 3000000 INFO @ Tue, 16 Jun 2020 09:35:43: 13000000 INFO @ Tue, 16 Jun 2020 09:35:44: 8000000 INFO @ Tue, 16 Jun 2020 09:35:48: 4000000 INFO @ Tue, 16 Jun 2020 09:35:49: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:35:49: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:35:49: #1 total tags in treatment: 13932275 INFO @ Tue, 16 Jun 2020 09:35:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:49: #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 09:35:49: #1 tags after filtering in treatment: 13932275 INFO @ Tue, 16 Jun 2020 09:35:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:50: 9000000 INFO @ Tue, 16 Jun 2020 09:35:50: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 09:35:50: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:50: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:35:50: #2 alternative fragment length(s) may be 1,28,546,580 bps INFO @ Tue, 16 Jun 2020 09:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:51: #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 09:35:51: #2 You may need to consider one of the other alternative d(s): 1,28,546,580 WARNING @ Tue, 16 Jun 2020 09:35:51: #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 09:35:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:54: 5000000 INFO @ Tue, 16 Jun 2020 09:35:56: 10000000 INFO @ Tue, 16 Jun 2020 09:36:00: 6000000 INFO @ Tue, 16 Jun 2020 09:36:02: 11000000 INFO @ Tue, 16 Jun 2020 09:36:06: 7000000 INFO @ Tue, 16 Jun 2020 09:36:08: 12000000 INFO @ Tue, 16 Jun 2020 09:36:12: 8000000 INFO @ Tue, 16 Jun 2020 09:36:14: 13000000 INFO @ Tue, 16 Jun 2020 09:36:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:18: 9000000 INFO @ Tue, 16 Jun 2020 09:36:20: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:36:20: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:36:20: #1 total tags in treatment: 13932275 INFO @ Tue, 16 Jun 2020 09:36:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:20: #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 09:36:20: #1 tags after filtering in treatment: 13932275 INFO @ Tue, 16 Jun 2020 09:36:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:21: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 09:36:21: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:36:21: #2 alternative fragment length(s) may be 1,28,546,580 bps INFO @ Tue, 16 Jun 2020 09:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:21: #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 09:36:21: #2 You may need to consider one of the other alternative d(s): 1,28,546,580 WARNING @ Tue, 16 Jun 2020 09:36:21: #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 09:36:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:24: 10000000 INFO @ Tue, 16 Jun 2020 09:36:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:30: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:36: 12000000 INFO @ Tue, 16 Jun 2020 09:36:42: 13000000 INFO @ Tue, 16 Jun 2020 09:36:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:47: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:36:47: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:36:47: #1 total tags in treatment: 13932275 INFO @ Tue, 16 Jun 2020 09:36:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:47: #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 09:36:47: #1 tags after filtering in treatment: 13932275 INFO @ Tue, 16 Jun 2020 09:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:48: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 09:36:48: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:48: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:36:48: #2 alternative fragment length(s) may be 1,28,546,580 bps INFO @ Tue, 16 Jun 2020 09:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:48: #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 09:36:48: #2 You may need to consider one of the other alternative d(s): 1,28,546,580 WARNING @ Tue, 16 Jun 2020 09:36:48: #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 09:36:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:56: 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 09:37:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529214/SRX529214.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling