Job ID = 6452377 SRX = SRX013017 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:50:45 prefetch.2.10.7: 1) Downloading 'SRR030283'... 2020-06-21T07:50:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:51:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:51:23 prefetch.2.10.7: 'SRR030283' is valid 2020-06-21T07:51:23 prefetch.2.10.7: 1) 'SRR030283' was downloaded successfully Read 4045663 spots for SRR030283/SRR030283.sra Written 4045663 spots for SRR030283/SRR030283.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: 00:00:40 4045663 reads; of these: 4045663 (100.00%) were unpaired; of these: 198814 (4.91%) aligned 0 times 3598435 (88.95%) aligned exactly 1 time 248414 (6.14%) aligned >1 times 95.09% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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_rmdupse_core] 377547 / 3846849 = 0.0981 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 16:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.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 16:53:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:37: 1000000 INFO @ Sun, 21 Jun 2020 16:53:41: 2000000 INFO @ Sun, 21 Jun 2020 16:53:46: 3000000 INFO @ Sun, 21 Jun 2020 16:53:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:48: #1 total tags in treatment: 3469302 INFO @ Sun, 21 Jun 2020 16:53:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:48: #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 16:53:49: #1 tags after filtering in treatment: 3468804 INFO @ Sun, 21 Jun 2020 16:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:49: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:49: #2 number of paired peaks: 8640 INFO @ Sun, 21 Jun 2020 16:53:49: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:49: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:49: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:49: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:49: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 16:53:49: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 16:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.05_model.r INFO @ Sun, 21 Jun 2020 16:53:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:58: #3 Call peaks for each chromosome... 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 16:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.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 16:54:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.05_summits.bed INFO @ Sun, 21 Jun 2020 16:54:03: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (6317 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:07: 1000000 INFO @ Sun, 21 Jun 2020 16:54:11: 2000000 INFO @ Sun, 21 Jun 2020 16:54:16: 3000000 INFO @ Sun, 21 Jun 2020 16:54:19: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:19: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:19: #1 total tags in treatment: 3469302 INFO @ Sun, 21 Jun 2020 16:54:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:19: #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 16:54:19: #1 tags after filtering in treatment: 3468804 INFO @ Sun, 21 Jun 2020 16:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:19: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:19: #2 number of paired peaks: 8640 INFO @ Sun, 21 Jun 2020 16:54:19: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:19: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:20: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:20: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:20: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 16:54:20: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 16:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.10_model.r INFO @ Sun, 21 Jun 2020 16:54:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:54:28: #3 Call peaks for each chromosome... 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 16:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.10_summits.bed INFO @ Sun, 21 Jun 2020 16:54:32: Done! INFO @ Sun, 21 Jun 2020 16:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.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 16:54:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:32: #1 read treatment tags... pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (5183 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:38: 1000000 INFO @ Sun, 21 Jun 2020 16:54:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:54:48: 3000000 INFO @ Sun, 21 Jun 2020 16:54:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:51: #1 total tags in treatment: 3469302 INFO @ Sun, 21 Jun 2020 16:54:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:51: #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 16:54:51: #1 tags after filtering in treatment: 3468804 INFO @ Sun, 21 Jun 2020 16:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:51: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:52: #2 number of paired peaks: 8640 INFO @ Sun, 21 Jun 2020 16:54:52: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:52: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:52: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:52: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:52: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 16:54:52: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 16:54:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.20_model.r INFO @ Sun, 21 Jun 2020 16:54:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:55:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013017/SRX013017.20_summits.bed INFO @ Sun, 21 Jun 2020 16:55:04: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (3470 records, 4 fields): 6 millis CompletedMACS2peakCalling