Job ID = 6367039 SRX = SRX2761384 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:19:31 prefetch.2.10.7: 1) Downloading 'SRR5476958'... 2020-06-15T23:19:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:47 prefetch.2.10.7: 'SRR5476958' is valid 2020-06-15T23:20:47 prefetch.2.10.7: 1) 'SRR5476958' was downloaded successfully Read 8878603 spots for SRR5476958/SRR5476958.sra Written 8878603 spots for SRR5476958/SRR5476958.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: 00:02:00 8878603 reads; of these: 8878603 (100.00%) were unpaired; of these: 539201 (6.07%) aligned 0 times 6210428 (69.95%) aligned exactly 1 time 2128974 (23.98%) aligned >1 times 93.93% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 1442912 / 8339402 = 0.1730 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 08:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.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 08:25:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:45: 1000000 INFO @ Tue, 16 Jun 2020 08:25:50: 2000000 INFO @ Tue, 16 Jun 2020 08:25:56: 3000000 INFO @ Tue, 16 Jun 2020 08:26:02: 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 08:26:08: 5000000 INFO @ Tue, 16 Jun 2020 08:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.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 08:26:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:14: 6000000 INFO @ Tue, 16 Jun 2020 08:26:15: 1000000 INFO @ Tue, 16 Jun 2020 08:26:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:20: #1 total tags in treatment: 6896490 INFO @ Tue, 16 Jun 2020 08:26:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:20: #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 08:26:20: #1 tags after filtering in treatment: 6896490 INFO @ Tue, 16 Jun 2020 08:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:20: 2000000 INFO @ Tue, 16 Jun 2020 08:26:21: #2 number of paired peaks: 828 WARNING @ Tue, 16 Jun 2020 08:26:21: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:21: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:26:21: #2 alternative fragment length(s) may be 3,57,578 bps INFO @ Tue, 16 Jun 2020 08:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:21: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:21: #2 You may need to consider one of the other alternative d(s): 3,57,578 WARNING @ Tue, 16 Jun 2020 08:26:21: #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 08:26:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:26: 3000000 INFO @ Tue, 16 Jun 2020 08:26:31: 4000000 INFO @ Tue, 16 Jun 2020 08:26:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:37: 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 08:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.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 08:26:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:42: 6000000 INFO @ Tue, 16 Jun 2020 08:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (813 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:44: 1000000 INFO @ Tue, 16 Jun 2020 08:26:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:47: #1 total tags in treatment: 6896490 INFO @ Tue, 16 Jun 2020 08:26:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:47: #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 08:26:47: #1 tags after filtering in treatment: 6896490 INFO @ Tue, 16 Jun 2020 08:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:48: #2 number of paired peaks: 828 WARNING @ Tue, 16 Jun 2020 08:26:48: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:48: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:26:48: #2 alternative fragment length(s) may be 3,57,578 bps INFO @ Tue, 16 Jun 2020 08:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:48: #2 You may need to consider one of the other alternative d(s): 3,57,578 WARNING @ Tue, 16 Jun 2020 08:26:48: #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 08:26:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:50: 2000000 INFO @ Tue, 16 Jun 2020 08:26:55: 3000000 INFO @ Tue, 16 Jun 2020 08:27:01: 4000000 INFO @ Tue, 16 Jun 2020 08:27:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:06: 5000000 INFO @ Tue, 16 Jun 2020 08:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (447 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:12: 6000000 INFO @ Tue, 16 Jun 2020 08:27:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:17: #1 total tags in treatment: 6896490 INFO @ Tue, 16 Jun 2020 08:27:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:17: #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 08:27:17: #1 tags after filtering in treatment: 6896490 INFO @ Tue, 16 Jun 2020 08:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:17: #2 number of paired peaks: 828 WARNING @ Tue, 16 Jun 2020 08:27:17: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:17: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:27:17: #2 alternative fragment length(s) may be 3,57,578 bps INFO @ Tue, 16 Jun 2020 08:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.20_model.r WARNING @ Tue, 16 Jun 2020 08:27:17: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:17: #2 You may need to consider one of the other alternative d(s): 3,57,578 WARNING @ Tue, 16 Jun 2020 08:27:17: #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 08:27:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:27:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761384/SRX2761384.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling