Job ID = 6455562 SRX = SRX287888 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:07:36 prefetch.2.10.7: 1) Downloading 'SRR870077'... 2020-06-21T10:07:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:23 prefetch.2.10.7: 1) 'SRR870077' was downloaded successfully Read 19464803 spots for SRR870077/SRR870077.sra Written 19464803 spots for SRR870077/SRR870077.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: 00:05:26 19464803 reads; of these: 19464803 (100.00%) were unpaired; of these: 1093415 (5.62%) aligned 0 times 13941414 (71.62%) aligned exactly 1 time 4429974 (22.76%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 2644580 / 18371388 = 0.1440 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 19:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.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 19:22:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:48: 1000000 INFO @ Sun, 21 Jun 2020 19:22:55: 2000000 INFO @ Sun, 21 Jun 2020 19:23:02: 3000000 INFO @ Sun, 21 Jun 2020 19:23:09: 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 19:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.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 19:23:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:16: 5000000 INFO @ Sun, 21 Jun 2020 19:23:19: 1000000 INFO @ Sun, 21 Jun 2020 19:23:24: 6000000 INFO @ Sun, 21 Jun 2020 19:23:26: 2000000 INFO @ Sun, 21 Jun 2020 19:23:32: 7000000 INFO @ Sun, 21 Jun 2020 19:23:34: 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 19:23:39: 8000000 INFO @ Sun, 21 Jun 2020 19:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.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 19:23:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:42: 4000000 INFO @ Sun, 21 Jun 2020 19:23:47: 9000000 INFO @ Sun, 21 Jun 2020 19:23:49: 1000000 INFO @ Sun, 21 Jun 2020 19:23:50: 5000000 INFO @ Sun, 21 Jun 2020 19:23:55: 10000000 INFO @ Sun, 21 Jun 2020 19:23:57: 2000000 INFO @ Sun, 21 Jun 2020 19:23:59: 6000000 INFO @ Sun, 21 Jun 2020 19:24:04: 11000000 INFO @ Sun, 21 Jun 2020 19:24:06: 3000000 INFO @ Sun, 21 Jun 2020 19:24:07: 7000000 INFO @ Sun, 21 Jun 2020 19:24:12: 12000000 INFO @ Sun, 21 Jun 2020 19:24:14: 4000000 INFO @ Sun, 21 Jun 2020 19:24:16: 8000000 INFO @ Sun, 21 Jun 2020 19:24:20: 13000000 INFO @ Sun, 21 Jun 2020 19:24:23: 5000000 INFO @ Sun, 21 Jun 2020 19:24:25: 9000000 INFO @ Sun, 21 Jun 2020 19:24:29: 14000000 INFO @ Sun, 21 Jun 2020 19:24:32: 6000000 INFO @ Sun, 21 Jun 2020 19:24:34: 10000000 INFO @ Sun, 21 Jun 2020 19:24:37: 15000000 INFO @ Sun, 21 Jun 2020 19:24:40: 7000000 INFO @ Sun, 21 Jun 2020 19:24:43: 11000000 INFO @ Sun, 21 Jun 2020 19:24:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:43: #1 total tags in treatment: 15726808 INFO @ Sun, 21 Jun 2020 19:24:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:43: #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 19:24:44: #1 tags after filtering in treatment: 15726808 INFO @ Sun, 21 Jun 2020 19:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:45: #2 number of paired peaks: 786 WARNING @ Sun, 21 Jun 2020 19:24:45: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:45: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:24:45: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.05_model.r INFO @ Sun, 21 Jun 2020 19:24:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:48: 8000000 INFO @ Sun, 21 Jun 2020 19:24:51: 12000000 INFO @ Sun, 21 Jun 2020 19:24:57: 9000000 INFO @ Sun, 21 Jun 2020 19:25:00: 13000000 INFO @ Sun, 21 Jun 2020 19:25:05: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:25:09: 14000000 INFO @ Sun, 21 Jun 2020 19:25:13: 11000000 INFO @ Sun, 21 Jun 2020 19:25:18: 15000000 INFO @ Sun, 21 Jun 2020 19:25:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:22: 12000000 INFO @ Sun, 21 Jun 2020 19:25:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:24: #1 total tags in treatment: 15726808 INFO @ Sun, 21 Jun 2020 19:25:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:24: #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 19:25:25: #1 tags after filtering in treatment: 15726808 INFO @ Sun, 21 Jun 2020 19:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:26: #2 number of paired peaks: 786 WARNING @ Sun, 21 Jun 2020 19:25:26: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:26: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:25:26: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:25:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.10_model.r INFO @ Sun, 21 Jun 2020 19:25:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:30: 13000000 INFO @ Sun, 21 Jun 2020 19:25:37: 14000000 INFO @ Sun, 21 Jun 2020 19:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.05_summits.bed INFO @ Sun, 21 Jun 2020 19:25:39: Done! pass1 - making usageList (628 chroms): 2 millis pass2 - checking and writing primary data (6439 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:25:45: 15000000 INFO @ Sun, 21 Jun 2020 19:25:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:51: #1 total tags in treatment: 15726808 INFO @ Sun, 21 Jun 2020 19:25:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:51: #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 19:25:52: #1 tags after filtering in treatment: 15726808 INFO @ Sun, 21 Jun 2020 19:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:53: #2 number of paired peaks: 786 WARNING @ Sun, 21 Jun 2020 19:25:53: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:53: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 19:25:53: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 19:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.20_model.r INFO @ Sun, 21 Jun 2020 19:25:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.10_summits.bed INFO @ Sun, 21 Jun 2020 19:26:19: Done! pass1 - making usageList (541 chroms): 2 millis pass2 - checking and writing primary data (4731 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287888/SRX287888.20_summits.bed INFO @ Sun, 21 Jun 2020 19:26:48: Done! pass1 - making usageList (446 chroms): 1 millis pass2 - checking and writing primary data (2774 records, 4 fields): 15 millis CompletedMACS2peakCalling