Job ID = 6456222 SRX = SRX331379 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:14 prefetch.2.10.7: 1) Downloading 'SRR947616'... 2020-06-21T10:35:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:16 prefetch.2.10.7: 'SRR947616' is valid 2020-06-21T10:37:16 prefetch.2.10.7: 1) 'SRR947616' was downloaded successfully Read 11897294 spots for SRR947616/SRR947616.sra Written 11897294 spots for SRR947616/SRR947616.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: 00:02:46 11897294 reads; of these: 11897294 (100.00%) were unpaired; of these: 1240082 (10.42%) aligned 0 times 8642126 (72.64%) aligned exactly 1 time 2015086 (16.94%) aligned >1 times 89.58% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1954404 / 10657212 = 0.1834 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 @ Sun, 21 Jun 2020 19:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:43:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:49: 1000000 INFO @ Sun, 21 Jun 2020 19:43:55: 2000000 INFO @ Sun, 21 Jun 2020 19:44:01: 3000000 INFO @ Sun, 21 Jun 2020 19:44:07: 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 @ Sun, 21 Jun 2020 19:44:13: 5000000 INFO @ Sun, 21 Jun 2020 19:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:44:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:19: 6000000 INFO @ Sun, 21 Jun 2020 19:44:20: 1000000 INFO @ Sun, 21 Jun 2020 19:44:25: 7000000 INFO @ Sun, 21 Jun 2020 19:44:27: 2000000 INFO @ Sun, 21 Jun 2020 19:44:33: 8000000 INFO @ Sun, 21 Jun 2020 19:44:33: 3000000 INFO @ Sun, 21 Jun 2020 19:44:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:37: #1 total tags in treatment: 8702808 INFO @ Sun, 21 Jun 2020 19:44:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:44:38: #1 tags after filtering in treatment: 8702793 INFO @ Sun, 21 Jun 2020 19:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:38: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 19:44:38: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:39: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 19:44:39: #2 alternative fragment length(s) may be 76,95,588 bps INFO @ Sun, 21 Jun 2020 19:44:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.05_model.r WARNING @ Sun, 21 Jun 2020 19:44:39: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:44:39: #2 You may need to consider one of the other alternative d(s): 76,95,588 WARNING @ Sun, 21 Jun 2020 19:44:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:44:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:40: 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 @ Sun, 21 Jun 2020 19:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:44:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:46: 5000000 INFO @ Sun, 21 Jun 2020 19:44:50: 1000000 INFO @ Sun, 21 Jun 2020 19:44:52: 6000000 INFO @ Sun, 21 Jun 2020 19:44:57: 2000000 INFO @ Sun, 21 Jun 2020 19:44:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:59: 7000000 INFO @ Sun, 21 Jun 2020 19:45:03: 3000000 INFO @ Sun, 21 Jun 2020 19:45:06: 8000000 INFO @ Sun, 21 Jun 2020 19:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.05_summits.bed INFO @ Sun, 21 Jun 2020 19:45:09: Done! pass1 - making usageList (466 chroms): 2 millis pass2 - checking and writing primary data (1312 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:45:10: 4000000 INFO @ Sun, 21 Jun 2020 19:45:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:11: #1 total tags in treatment: 8702808 INFO @ Sun, 21 Jun 2020 19:45:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:45:12: #1 tags after filtering in treatment: 8702793 INFO @ Sun, 21 Jun 2020 19:45:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:12: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 19:45:12: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:12: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 19:45:12: #2 alternative fragment length(s) may be 76,95,588 bps INFO @ Sun, 21 Jun 2020 19:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.10_model.r WARNING @ Sun, 21 Jun 2020 19:45:12: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:45:12: #2 You may need to consider one of the other alternative d(s): 76,95,588 WARNING @ Sun, 21 Jun 2020 19:45:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:45:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:16: 5000000 INFO @ Sun, 21 Jun 2020 19:45:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:45:28: 7000000 INFO @ Sun, 21 Jun 2020 19:45:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:35: 8000000 INFO @ Sun, 21 Jun 2020 19:45:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:39: #1 total tags in treatment: 8702808 INFO @ Sun, 21 Jun 2020 19:45:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:45:40: #1 tags after filtering in treatment: 8702793 INFO @ Sun, 21 Jun 2020 19:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:40: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 19:45:40: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:40: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 19:45:40: #2 alternative fragment length(s) may be 76,95,588 bps INFO @ Sun, 21 Jun 2020 19:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.20_model.r WARNING @ Sun, 21 Jun 2020 19:45:40: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:45:40: #2 You may need to consider one of the other alternative d(s): 76,95,588 WARNING @ Sun, 21 Jun 2020 19:45:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:45:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.10_summits.bed INFO @ Sun, 21 Jun 2020 19:45:43: Done! pass1 - making usageList (301 chroms): 1 millis pass2 - checking and writing primary data (583 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:46:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331379/SRX331379.20_summits.bed INFO @ Sun, 21 Jun 2020 19:46:11: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 6 millis CompletedMACS2peakCalling