Job ID = 6366902 SRX = SRX257647 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 'SRR800658'... 2020-06-15T23:04:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:22 prefetch.2.10.7: 1) 'SRR800658' was downloaded successfully Read 17594324 spots for SRR800658/SRR800658.sra Written 17594324 spots for SRR800658/SRR800658.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: 00:04:09 17594324 reads; of these: 17594324 (100.00%) were unpaired; of these: 311802 (1.77%) aligned 0 times 14393704 (81.81%) aligned exactly 1 time 2888818 (16.42%) aligned >1 times 98.23% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 10020081 / 17282522 = 0.5798 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 08:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.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 08:15:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:23: 1000000 INFO @ Tue, 16 Jun 2020 08:15:28: 2000000 INFO @ Tue, 16 Jun 2020 08:15:34: 3000000 INFO @ Tue, 16 Jun 2020 08:15:39: 4000000 INFO @ Tue, 16 Jun 2020 08:15:44: 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 08:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.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 08:15:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:50: 6000000 INFO @ Tue, 16 Jun 2020 08:15:53: 1000000 INFO @ Tue, 16 Jun 2020 08:15:55: 7000000 INFO @ Tue, 16 Jun 2020 08:15:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:57: #1 total tags in treatment: 7262441 INFO @ Tue, 16 Jun 2020 08:15:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:57: #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 08:15:57: #1 tags after filtering in treatment: 7262441 INFO @ Tue, 16 Jun 2020 08:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:57: #2 number of paired peaks: 569 WARNING @ Tue, 16 Jun 2020 08:15:57: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:57: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:15:57: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:57: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:15:57: #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 08:15:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:59: 2000000 INFO @ Tue, 16 Jun 2020 08:16:04: 3000000 INFO @ Tue, 16 Jun 2020 08:16:09: 4000000 INFO @ Tue, 16 Jun 2020 08:16:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:14: 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 08:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.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 08:16:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:20: 6000000 INFO @ Tue, 16 Jun 2020 08:16:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (986 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:24: 1000000 INFO @ Tue, 16 Jun 2020 08:16:25: 7000000 INFO @ Tue, 16 Jun 2020 08:16:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:26: #1 total tags in treatment: 7262441 INFO @ Tue, 16 Jun 2020 08:16:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:26: #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 08:16:26: #1 tags after filtering in treatment: 7262441 INFO @ Tue, 16 Jun 2020 08:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:27: #2 number of paired peaks: 569 WARNING @ Tue, 16 Jun 2020 08:16:27: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:27: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:16:27: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.10_model.r WARNING @ Tue, 16 Jun 2020 08:16:27: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:27: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:16:27: #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 08:16:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:31: 2000000 INFO @ Tue, 16 Jun 2020 08:16:37: 3000000 INFO @ Tue, 16 Jun 2020 08:16:43: 4000000 INFO @ Tue, 16 Jun 2020 08:16:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:48: 5000000 INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (633 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:54: 6000000 INFO @ Tue, 16 Jun 2020 08:17:00: 7000000 INFO @ Tue, 16 Jun 2020 08:17:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:02: #1 total tags in treatment: 7262441 INFO @ Tue, 16 Jun 2020 08:17:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:02: #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 08:17:02: #1 tags after filtering in treatment: 7262441 INFO @ Tue, 16 Jun 2020 08:17:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:02: #2 number of paired peaks: 569 WARNING @ Tue, 16 Jun 2020 08:17:02: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:03: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:17:03: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.20_model.r WARNING @ Tue, 16 Jun 2020 08:17:03: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:03: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:17:03: #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 08:17:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257647/SRX257647.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 1 millis CompletedMACS2peakCalling