Job ID = 6454407 SRX = SRX2035279 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:48 prefetch.2.10.7: 1) Downloading 'SRR4044403'... 2020-06-21T09:09:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:13:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:13:39 prefetch.2.10.7: 1) 'SRR4044403' was downloaded successfully 2020-06-21T09:13:39 prefetch.2.10.7: 'SRR4044403' has 0 unresolved dependencies Read 26727264 spots for SRR4044403/SRR4044403.sra Written 26727264 spots for SRR4044403/SRR4044403.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: 00:08:55 26727264 reads; of these: 26727264 (100.00%) were unpaired; of these: 1035766 (3.88%) aligned 0 times 20943484 (78.36%) aligned exactly 1 time 4748014 (17.76%) aligned >1 times 96.12% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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 12 files... [bam_rmdupse_core] 8057250 / 25691498 = 0.3136 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 18:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.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 18:29:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:02: 1000000 INFO @ Sun, 21 Jun 2020 18:30:08: 2000000 INFO @ Sun, 21 Jun 2020 18:30:14: 3000000 INFO @ Sun, 21 Jun 2020 18:30:21: 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 18:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.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 18:30:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:27: 5000000 INFO @ Sun, 21 Jun 2020 18:30:35: 6000000 INFO @ Sun, 21 Jun 2020 18:30:35: 1000000 INFO @ Sun, 21 Jun 2020 18:30:43: 7000000 INFO @ Sun, 21 Jun 2020 18:30:44: 2000000 INFO @ Sun, 21 Jun 2020 18:30:50: 8000000 INFO @ Sun, 21 Jun 2020 18:30:53: 3000000 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 18:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.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 18:30:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:58: 9000000 INFO @ Sun, 21 Jun 2020 18:31:02: 4000000 INFO @ Sun, 21 Jun 2020 18:31:05: 1000000 INFO @ Sun, 21 Jun 2020 18:31:06: 10000000 INFO @ Sun, 21 Jun 2020 18:31:11: 5000000 INFO @ Sun, 21 Jun 2020 18:31:13: 2000000 INFO @ Sun, 21 Jun 2020 18:31:15: 11000000 INFO @ Sun, 21 Jun 2020 18:31:20: 6000000 INFO @ Sun, 21 Jun 2020 18:31:22: 3000000 INFO @ Sun, 21 Jun 2020 18:31:23: 12000000 INFO @ Sun, 21 Jun 2020 18:31:29: 7000000 INFO @ Sun, 21 Jun 2020 18:31:31: 13000000 INFO @ Sun, 21 Jun 2020 18:31:31: 4000000 INFO @ Sun, 21 Jun 2020 18:31:37: 8000000 INFO @ Sun, 21 Jun 2020 18:31:39: 14000000 INFO @ Sun, 21 Jun 2020 18:31:40: 5000000 INFO @ Sun, 21 Jun 2020 18:31:46: 9000000 INFO @ Sun, 21 Jun 2020 18:31:47: 15000000 INFO @ Sun, 21 Jun 2020 18:31:49: 6000000 INFO @ Sun, 21 Jun 2020 18:31:55: 10000000 INFO @ Sun, 21 Jun 2020 18:31:55: 16000000 INFO @ Sun, 21 Jun 2020 18:31:58: 7000000 INFO @ Sun, 21 Jun 2020 18:32:04: 17000000 INFO @ Sun, 21 Jun 2020 18:32:04: 11000000 INFO @ Sun, 21 Jun 2020 18:32:07: 8000000 INFO @ Sun, 21 Jun 2020 18:32:09: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:32:09: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:32:09: #1 total tags in treatment: 17634248 INFO @ Sun, 21 Jun 2020 18:32:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:09: #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 18:32:10: #1 tags after filtering in treatment: 17634244 INFO @ Sun, 21 Jun 2020 18:32:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:11: #2 number of paired peaks: 3686 INFO @ Sun, 21 Jun 2020 18:32:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:11: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:32:11: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.05_model.r WARNING @ Sun, 21 Jun 2020 18:32:11: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:11: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sun, 21 Jun 2020 18:32:11: #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 18:32:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:32:12: 12000000 INFO @ Sun, 21 Jun 2020 18:32:16: 9000000 INFO @ Sun, 21 Jun 2020 18:32:21: 13000000 INFO @ Sun, 21 Jun 2020 18:32:25: 10000000 INFO @ Sun, 21 Jun 2020 18:32:31: 14000000 INFO @ Sun, 21 Jun 2020 18:32:34: 11000000 INFO @ Sun, 21 Jun 2020 18:32:40: 15000000 INFO @ Sun, 21 Jun 2020 18:32:42: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:32:49: 16000000 INFO @ Sun, 21 Jun 2020 18:32:51: 13000000 INFO @ Sun, 21 Jun 2020 18:32:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:58: 17000000 INFO @ Sun, 21 Jun 2020 18:33:00: 14000000 INFO @ Sun, 21 Jun 2020 18:33:04: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:33:04: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:33:04: #1 total tags in treatment: 17634248 INFO @ Sun, 21 Jun 2020 18:33:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:04: #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 18:33:05: #1 tags after filtering in treatment: 17634244 INFO @ Sun, 21 Jun 2020 18:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:06: #2 number of paired peaks: 3686 INFO @ Sun, 21 Jun 2020 18:33:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:07: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:33:07: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:07: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:07: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sun, 21 Jun 2020 18:33:07: #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 18:33:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:09: 15000000 INFO @ Sun, 21 Jun 2020 18:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:12: Done! pass1 - making usageList (639 chroms): 3 millis pass2 - checking and writing primary data (16011 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:18: 16000000 INFO @ Sun, 21 Jun 2020 18:33:26: 17000000 INFO @ Sun, 21 Jun 2020 18:33:31: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:33:31: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:33:31: #1 total tags in treatment: 17634248 INFO @ Sun, 21 Jun 2020 18:33:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:31: #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 18:33:32: #1 tags after filtering in treatment: 17634244 INFO @ Sun, 21 Jun 2020 18:33:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:33: #2 number of paired peaks: 3686 INFO @ Sun, 21 Jun 2020 18:33:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:33: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:33:33: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:33:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.20_model.r WARNING @ Sun, 21 Jun 2020 18:33:33: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:33: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sun, 21 Jun 2020 18:33:33: #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 18:33:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:08: Done! pass1 - making usageList (505 chroms): 3 millis pass2 - checking and writing primary data (12223 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035279/SRX2035279.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:33: Done! pass1 - making usageList (333 chroms): 2 millis pass2 - checking and writing primary data (8421 records, 4 fields): 17 millis CompletedMACS2peakCalling