Job ID = 6452547 SRX = SRX016156 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:51 prefetch.2.10.7: 1) Downloading 'SRR034718'... 2020-06-21T07:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:41:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:41:46 prefetch.2.10.7: 'SRR034718' is valid 2020-06-21T07:41:46 prefetch.2.10.7: 1) 'SRR034718' was downloaded successfully Read 14583545 spots for SRR034718/SRR034718.sra Written 14583545 spots for SRR034718/SRR034718.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: 00:02:53 14583545 reads; of these: 14583545 (100.00%) were unpaired; of these: 564084 (3.87%) aligned 0 times 10968246 (75.21%) aligned exactly 1 time 3051215 (20.92%) aligned >1 times 96.13% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 4690779 / 14019461 = 0.3346 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 16:48:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.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 16:48:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:48:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:01: 1000000 INFO @ Sun, 21 Jun 2020 16:49:06: 2000000 INFO @ Sun, 21 Jun 2020 16:49:12: 3000000 INFO @ Sun, 21 Jun 2020 16:49:17: 4000000 INFO @ Sun, 21 Jun 2020 16:49:23: 5000000 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 16:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.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 16:49:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:29: 6000000 INFO @ Sun, 21 Jun 2020 16:49:31: 1000000 INFO @ Sun, 21 Jun 2020 16:49:35: 7000000 INFO @ Sun, 21 Jun 2020 16:49:38: 2000000 INFO @ Sun, 21 Jun 2020 16:49:42: 8000000 INFO @ Sun, 21 Jun 2020 16:49:44: 3000000 INFO @ Sun, 21 Jun 2020 16:49:49: 9000000 INFO @ Sun, 21 Jun 2020 16:49:51: 4000000 INFO @ Sun, 21 Jun 2020 16:49:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:51: #1 total tags in treatment: 9328682 INFO @ Sun, 21 Jun 2020 16:49:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:51: #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 16:49:52: #1 tags after filtering in treatment: 9328656 INFO @ Sun, 21 Jun 2020 16:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:52: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:52: #2 number of paired peaks: 594 WARNING @ Sun, 21 Jun 2020 16:49:52: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sun, 21 Jun 2020 16:49:52: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:52: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:52: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:52: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:52: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 16:49:52: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 16:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.05_model.r INFO @ Sun, 21 Jun 2020 16:49:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:52: #3 Pre-compute pvalue-qvalue table... 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 16:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.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 16:49:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:57: 5000000 INFO @ Sun, 21 Jun 2020 16:50:02: 1000000 INFO @ Sun, 21 Jun 2020 16:50:03: 6000000 INFO @ Sun, 21 Jun 2020 16:50:08: 2000000 INFO @ Sun, 21 Jun 2020 16:50:10: 7000000 INFO @ Sun, 21 Jun 2020 16:50:15: 3000000 INFO @ Sun, 21 Jun 2020 16:50:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:17: 8000000 INFO @ Sun, 21 Jun 2020 16:50:22: 4000000 INFO @ Sun, 21 Jun 2020 16:50:23: 9000000 INFO @ Sun, 21 Jun 2020 16:50:26: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:26: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:26: #1 total tags in treatment: 9328682 INFO @ Sun, 21 Jun 2020 16:50:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:26: #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 16:50:26: #1 tags after filtering in treatment: 9328656 INFO @ Sun, 21 Jun 2020 16:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:26: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:27: #2 number of paired peaks: 594 WARNING @ Sun, 21 Jun 2020 16:50:27: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sun, 21 Jun 2020 16:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:27: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:27: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:27: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:27: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 16:50:27: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 16:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.10_model.r INFO @ Sun, 21 Jun 2020 16:50:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.05_summits.bed INFO @ Sun, 21 Jun 2020 16:50:27: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (2093 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:28: 5000000 INFO @ Sun, 21 Jun 2020 16:50:34: 6000000 INFO @ Sun, 21 Jun 2020 16:50:41: 7000000 INFO @ Sun, 21 Jun 2020 16:50:47: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:50:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:53: 9000000 INFO @ Sun, 21 Jun 2020 16:50:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:55: #1 total tags in treatment: 9328682 INFO @ Sun, 21 Jun 2020 16:50:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:55: #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 16:50:56: #1 tags after filtering in treatment: 9328656 INFO @ Sun, 21 Jun 2020 16:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:56: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:56: #2 number of paired peaks: 594 WARNING @ Sun, 21 Jun 2020 16:50:56: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sun, 21 Jun 2020 16:50:56: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:56: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:56: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:56: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:56: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 16:50:56: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 16:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.20_model.r INFO @ Sun, 21 Jun 2020 16:50:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.10_summits.bed INFO @ Sun, 21 Jun 2020 16:51:01: Done! pass1 - making usageList (281 chroms): 1 millis pass2 - checking and writing primary data (943 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:51:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016156/SRX016156.20_summits.bed INFO @ Sun, 21 Jun 2020 16:51:31: Done! pass1 - making usageList (191 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 8 millis CompletedMACS2peakCalling