Job ID = 6453037 SRX = SRX100253 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:00:23 prefetch.2.10.7: 1) Downloading 'SRR351347'... 2020-06-21T08:00:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:51 prefetch.2.10.7: 'SRR351347' is valid 2020-06-21T08:01:51 prefetch.2.10.7: 1) 'SRR351347' was downloaded successfully Read 7551057 spots for SRR351347/SRR351347.sra Written 7551057 spots for SRR351347/SRR351347.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: 00:01:05 7551057 reads; of these: 7551057 (100.00%) were unpaired; of these: 4674273 (61.90%) aligned 0 times 2081833 (27.57%) aligned exactly 1 time 794951 (10.53%) aligned >1 times 38.10% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 780842 / 2876784 = 0.2714 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 17:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.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 17:04:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:51: 1000000 INFO @ Sun, 21 Jun 2020 17:04:56: 2000000 INFO @ Sun, 21 Jun 2020 17:04:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:04:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:04:57: #1 total tags in treatment: 2095942 INFO @ Sun, 21 Jun 2020 17:04:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:04:57: #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 17:04:57: #1 tags after filtering in treatment: 2095645 INFO @ Sun, 21 Jun 2020 17:04:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:04:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:04:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:04:57: #2 number of paired peaks: 2603 INFO @ Sun, 21 Jun 2020 17:04:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:04:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:04:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:04:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:04:57: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 17:04:57: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 17:04:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.05_model.r INFO @ Sun, 21 Jun 2020 17:04:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:04:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:05:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.05_summits.bed INFO @ Sun, 21 Jun 2020 17:05:05: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (2757 records, 4 fields): 10 millis CompletedMACS2peakCalling 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 17:05:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.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 17:05:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:22: 1000000 INFO @ Sun, 21 Jun 2020 17:05:28: 2000000 INFO @ Sun, 21 Jun 2020 17:05:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:05:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:05:28: #1 total tags in treatment: 2095942 INFO @ Sun, 21 Jun 2020 17:05:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:28: #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 17:05:28: #1 tags after filtering in treatment: 2095645 INFO @ Sun, 21 Jun 2020 17:05:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:29: #2 number of paired peaks: 2603 INFO @ Sun, 21 Jun 2020 17:05:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:29: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 17:05:29: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 17:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.10_model.r INFO @ Sun, 21 Jun 2020 17:05:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:05:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.10_summits.bed INFO @ Sun, 21 Jun 2020 17:05:37: Done! pass1 - making usageList (137 chroms): 2 millis pass2 - checking and writing primary data (2010 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 17:05:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.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 17:05:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:05:56: 2000000 INFO @ Sun, 21 Jun 2020 17:05:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:05:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:05:57: #1 total tags in treatment: 2095942 INFO @ Sun, 21 Jun 2020 17:05:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:57: #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 17:05:57: #1 tags after filtering in treatment: 2095645 INFO @ Sun, 21 Jun 2020 17:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:57: #2 number of paired peaks: 2603 INFO @ Sun, 21 Jun 2020 17:05:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:57: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 17:05:57: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 17:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.20_model.r INFO @ Sun, 21 Jun 2020 17:05:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:06:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX100253/SRX100253.20_summits.bed INFO @ Sun, 21 Jun 2020 17:06:05: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (1377 records, 4 fields): 5 millis CompletedMACS2peakCalling