Job ID = 6455156 SRX = SRX2804218 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:25 prefetch.2.10.7: 1) Downloading 'SRR5534646'... 2020-06-21T09:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:08 prefetch.2.10.7: 1) 'SRR5534646' was downloaded successfully 2020-06-21T09:51:08 prefetch.2.10.7: 'SRR5534646' has 0 unresolved dependencies Read 31725441 spots for SRR5534646/SRR5534646.sra Written 31725441 spots for SRR5534646/SRR5534646.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: 00:06:54 31725441 reads; of these: 31725441 (100.00%) were unpaired; of these: 9249551 (29.15%) aligned 0 times 16452469 (51.86%) aligned exactly 1 time 6023421 (18.99%) aligned >1 times 70.85% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 6404780 / 22475890 = 0.2850 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 19:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.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 19:05:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:29: 1000000 INFO @ Sun, 21 Jun 2020 19:05:35: 2000000 INFO @ Sun, 21 Jun 2020 19:05:41: 3000000 INFO @ Sun, 21 Jun 2020 19:05:47: 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 @ Sun, 21 Jun 2020 19:05:53: 5000000 INFO @ Sun, 21 Jun 2020 19:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.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 19:05:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:59: 6000000 INFO @ Sun, 21 Jun 2020 19:06:00: 1000000 INFO @ Sun, 21 Jun 2020 19:06:05: 7000000 INFO @ Sun, 21 Jun 2020 19:06:06: 2000000 INFO @ Sun, 21 Jun 2020 19:06:11: 8000000 INFO @ Sun, 21 Jun 2020 19:06:12: 3000000 INFO @ Sun, 21 Jun 2020 19:06:17: 9000000 INFO @ Sun, 21 Jun 2020 19:06:18: 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 19:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.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 19:06:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:23: 10000000 INFO @ Sun, 21 Jun 2020 19:06:24: 5000000 INFO @ Sun, 21 Jun 2020 19:06:30: 11000000 INFO @ Sun, 21 Jun 2020 19:06:30: 1000000 INFO @ Sun, 21 Jun 2020 19:06:30: 6000000 INFO @ Sun, 21 Jun 2020 19:06:36: 12000000 INFO @ Sun, 21 Jun 2020 19:06:36: 2000000 INFO @ Sun, 21 Jun 2020 19:06:37: 7000000 INFO @ Sun, 21 Jun 2020 19:06:43: 3000000 INFO @ Sun, 21 Jun 2020 19:06:43: 13000000 INFO @ Sun, 21 Jun 2020 19:06:43: 8000000 INFO @ Sun, 21 Jun 2020 19:06:49: 14000000 INFO @ Sun, 21 Jun 2020 19:06:49: 4000000 INFO @ Sun, 21 Jun 2020 19:06:50: 9000000 INFO @ Sun, 21 Jun 2020 19:06:55: 5000000 INFO @ Sun, 21 Jun 2020 19:06:56: 15000000 INFO @ Sun, 21 Jun 2020 19:06:56: 10000000 INFO @ Sun, 21 Jun 2020 19:07:02: 6000000 INFO @ Sun, 21 Jun 2020 19:07:02: 16000000 INFO @ Sun, 21 Jun 2020 19:07:02: 11000000 INFO @ Sun, 21 Jun 2020 19:07:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:07:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:07:03: #1 total tags in treatment: 16071110 INFO @ Sun, 21 Jun 2020 19:07:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:03: #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 19:07:04: #1 tags after filtering in treatment: 16071109 INFO @ Sun, 21 Jun 2020 19:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:05: #2 number of paired peaks: 885 WARNING @ Sun, 21 Jun 2020 19:07:05: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:05: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:07:05: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 19:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.05_model.r INFO @ Sun, 21 Jun 2020 19:07:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:08: 7000000 INFO @ Sun, 21 Jun 2020 19:07:09: 12000000 INFO @ Sun, 21 Jun 2020 19:07:14: 8000000 INFO @ Sun, 21 Jun 2020 19:07:16: 13000000 INFO @ Sun, 21 Jun 2020 19:07:20: 9000000 INFO @ Sun, 21 Jun 2020 19:07:22: 14000000 INFO @ Sun, 21 Jun 2020 19:07:26: 10000000 INFO @ Sun, 21 Jun 2020 19:07:28: 15000000 INFO @ Sun, 21 Jun 2020 19:07:32: 11000000 INFO @ Sun, 21 Jun 2020 19:07:35: 16000000 INFO @ Sun, 21 Jun 2020 19:07:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:07:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:07:36: #1 total tags in treatment: 16071110 INFO @ Sun, 21 Jun 2020 19:07:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:36: #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 19:07:36: #1 tags after filtering in treatment: 16071109 INFO @ Sun, 21 Jun 2020 19:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:38: #2 number of paired peaks: 885 WARNING @ Sun, 21 Jun 2020 19:07:38: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:38: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:07:38: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 19:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.10_model.r INFO @ Sun, 21 Jun 2020 19:07:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:38: 12000000 INFO @ Sun, 21 Jun 2020 19:07:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:44: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:07:50: 14000000 INFO @ Sun, 21 Jun 2020 19:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.05_summits.bed INFO @ Sun, 21 Jun 2020 19:07:54: Done! pass1 - making usageList (727 chroms): 2 millis pass2 - checking and writing primary data (7131 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:56: 15000000 INFO @ Sun, 21 Jun 2020 19:08:02: 16000000 INFO @ Sun, 21 Jun 2020 19:08:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:08:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:08:02: #1 total tags in treatment: 16071110 INFO @ Sun, 21 Jun 2020 19:08:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:02: #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 19:08:03: #1 tags after filtering in treatment: 16071109 INFO @ Sun, 21 Jun 2020 19:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:04: #2 number of paired peaks: 885 WARNING @ Sun, 21 Jun 2020 19:08:04: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Sun, 21 Jun 2020 19:08:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:04: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:08:04: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 19:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.20_model.r INFO @ Sun, 21 Jun 2020 19:08:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.10_summits.bed INFO @ Sun, 21 Jun 2020 19:08:26: Done! pass1 - making usageList (635 chroms): 2 millis pass2 - checking and writing primary data (4887 records, 4 fields): 47 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:08:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804218/SRX2804218.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:52: Done! pass1 - making usageList (521 chroms): 2 millis pass2 - checking and writing primary data (3157 records, 4 fields): 31 millis CompletedMACS2peakCalling