Job ID = 6452930 SRX = SRX050597 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:45:21 prefetch.2.10.7: 1) Downloading 'SRR139079'... 2020-06-21T07:45:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:50:05 prefetch.2.10.7: 'SRR139079' is valid 2020-06-21T07:50:05 prefetch.2.10.7: 1) 'SRR139079' was downloaded successfully Read 15476459 spots for SRR139079/SRR139079.sra Written 15476459 spots for SRR139079/SRR139079.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: 00:03:24 15476459 reads; of these: 15476459 (100.00%) were unpaired; of these: 614498 (3.97%) aligned 0 times 10537041 (68.08%) aligned exactly 1 time 4324920 (27.95%) aligned >1 times 96.03% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 2089263 / 14861961 = 0.1406 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 16:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.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 16:57:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:03: 1000000 INFO @ Sun, 21 Jun 2020 16:58:08: 2000000 INFO @ Sun, 21 Jun 2020 16:58:12: 3000000 INFO @ Sun, 21 Jun 2020 16:58:17: 4000000 INFO @ Sun, 21 Jun 2020 16:58:22: 5000000 INFO @ Sun, 21 Jun 2020 16:58:26: 6000000 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 16:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.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 16:58:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:31: 7000000 INFO @ Sun, 21 Jun 2020 16:58:34: 1000000 INFO @ Sun, 21 Jun 2020 16:58:35: 8000000 INFO @ Sun, 21 Jun 2020 16:58:39: 2000000 INFO @ Sun, 21 Jun 2020 16:58:40: 9000000 INFO @ Sun, 21 Jun 2020 16:58:44: 3000000 INFO @ Sun, 21 Jun 2020 16:58:44: 10000000 INFO @ Sun, 21 Jun 2020 16:58:49: 4000000 INFO @ Sun, 21 Jun 2020 16:58:49: 11000000 INFO @ Sun, 21 Jun 2020 16:58:54: 12000000 INFO @ Sun, 21 Jun 2020 16:58:54: 5000000 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 16:58:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:58: #1 total tags in treatment: 12772698 INFO @ Sun, 21 Jun 2020 16:58:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:58: #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 16:58:58: #1 tags after filtering in treatment: 12772610 INFO @ Sun, 21 Jun 2020 16:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:58: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.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 16:58:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:59: 6000000 INFO @ Sun, 21 Jun 2020 16:58:59: #2 number of paired peaks: 867 WARNING @ Sun, 21 Jun 2020 16:58:59: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Sun, 21 Jun 2020 16:58:59: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:59: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:59: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:59: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:59: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 16:58:59: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 16:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.05_model.r INFO @ Sun, 21 Jun 2020 16:58:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:04: 1000000 INFO @ Sun, 21 Jun 2020 16:59:04: 7000000 INFO @ Sun, 21 Jun 2020 16:59:09: 2000000 INFO @ Sun, 21 Jun 2020 16:59:09: 8000000 INFO @ Sun, 21 Jun 2020 16:59:14: 3000000 INFO @ Sun, 21 Jun 2020 16:59:14: 9000000 INFO @ Sun, 21 Jun 2020 16:59:19: 4000000 INFO @ Sun, 21 Jun 2020 16:59:19: 10000000 INFO @ Sun, 21 Jun 2020 16:59:24: 5000000 INFO @ Sun, 21 Jun 2020 16:59:25: 11000000 INFO @ Sun, 21 Jun 2020 16:59:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:29: 6000000 INFO @ Sun, 21 Jun 2020 16:59:30: 12000000 INFO @ Sun, 21 Jun 2020 16:59:34: 7000000 INFO @ Sun, 21 Jun 2020 16:59:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:59:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:59:34: #1 total tags in treatment: 12772698 INFO @ Sun, 21 Jun 2020 16:59:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:34: #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 16:59:35: #1 tags after filtering in treatment: 12772610 INFO @ Sun, 21 Jun 2020 16:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:35: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:36: #2 number of paired peaks: 867 WARNING @ Sun, 21 Jun 2020 16:59:36: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Sun, 21 Jun 2020 16:59:36: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:36: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:36: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:36: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:36: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 16:59:36: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 16:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.10_model.r INFO @ Sun, 21 Jun 2020 16:59:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:39: 8000000 INFO @ Sun, 21 Jun 2020 16:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.05_summits.bed INFO @ Sun, 21 Jun 2020 16:59:40: Done! pass1 - making usageList (606 chroms): 2 millis pass2 - checking and writing primary data (3764 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:59:44: 9000000 INFO @ Sun, 21 Jun 2020 16:59:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:59:54: 11000000 INFO @ Sun, 21 Jun 2020 16:59:59: 12000000 INFO @ Sun, 21 Jun 2020 17:00:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:04: #1 total tags in treatment: 12772698 INFO @ Sun, 21 Jun 2020 17:00:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:04: #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 17:00:04: #1 tags after filtering in treatment: 12772610 INFO @ Sun, 21 Jun 2020 17:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:05: #2 number of paired peaks: 867 WARNING @ Sun, 21 Jun 2020 17:00:05: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:05: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:00:05: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 17:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.20_model.r INFO @ Sun, 21 Jun 2020 17:00:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.10_summits.bed INFO @ Sun, 21 Jun 2020 17:00:15: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (1531 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:00:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050597/SRX050597.20_summits.bed INFO @ Sun, 21 Jun 2020 17:00:46: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 7 millis CompletedMACS2peakCalling