Job ID = 6452949 SRX = SRX059817 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:58:29 prefetch.2.10.7: 1) Downloading 'SRR191859'... 2020-06-21T07:58:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:05:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:05:04 prefetch.2.10.7: 1) 'SRR191859' was downloaded successfully Read 11397432 spots for SRR191859/SRR191859.sra Written 11397432 spots for SRR191859/SRR191859.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: 00:05:33 11397432 reads; of these: 11397432 (100.00%) were unpaired; of these: 206380 (1.81%) aligned 0 times 9360396 (82.13%) aligned exactly 1 time 1830656 (16.06%) aligned >1 times 98.19% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 1088680 / 11191052 = 0.0973 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 17:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.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 17:16:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:24: 1000000 INFO @ Sun, 21 Jun 2020 17:16:34: 2000000 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 17:16:43: 3000000 INFO @ Sun, 21 Jun 2020 17:16:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.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 17:16:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:55: 4000000 INFO @ Sun, 21 Jun 2020 17:16:55: 1000000 INFO @ Sun, 21 Jun 2020 17:17:06: 5000000 INFO @ Sun, 21 Jun 2020 17:17:06: 2000000 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 17:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.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 17:17:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:17: 6000000 INFO @ Sun, 21 Jun 2020 17:17:17: 3000000 INFO @ Sun, 21 Jun 2020 17:17:26: 1000000 INFO @ Sun, 21 Jun 2020 17:17:28: 7000000 INFO @ Sun, 21 Jun 2020 17:17:28: 4000000 INFO @ Sun, 21 Jun 2020 17:17:37: 2000000 INFO @ Sun, 21 Jun 2020 17:17:39: 5000000 INFO @ Sun, 21 Jun 2020 17:17:39: 8000000 INFO @ Sun, 21 Jun 2020 17:17:48: 3000000 INFO @ Sun, 21 Jun 2020 17:17:50: 6000000 INFO @ Sun, 21 Jun 2020 17:17:51: 9000000 INFO @ Sun, 21 Jun 2020 17:17:59: 4000000 INFO @ Sun, 21 Jun 2020 17:18:01: 7000000 INFO @ Sun, 21 Jun 2020 17:18:02: 10000000 INFO @ Sun, 21 Jun 2020 17:18:04: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 17:18:04: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 17:18:04: #1 total tags in treatment: 10102372 INFO @ Sun, 21 Jun 2020 17:18:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:04: #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 17:18:04: #1 tags after filtering in treatment: 10102356 INFO @ Sun, 21 Jun 2020 17:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:05: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 17:18:05: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 17:18:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:05: #2 predicted fragment length is 184 bps INFO @ Sun, 21 Jun 2020 17:18:05: #2 alternative fragment length(s) may be 184 bps INFO @ Sun, 21 Jun 2020 17:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.05_model.r WARNING @ Sun, 21 Jun 2020 17:18:05: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:18:05: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Sun, 21 Jun 2020 17:18:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:18:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:11: 5000000 INFO @ Sun, 21 Jun 2020 17:18:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:18:23: 6000000 INFO @ Sun, 21 Jun 2020 17:18:23: 9000000 INFO @ Sun, 21 Jun 2020 17:18:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:18:34: 10000000 INFO @ Sun, 21 Jun 2020 17:18:34: 7000000 INFO @ Sun, 21 Jun 2020 17:18:35: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 17:18:35: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 17:18:35: #1 total tags in treatment: 10102372 INFO @ Sun, 21 Jun 2020 17:18:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:35: #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 17:18:35: #1 tags after filtering in treatment: 10102356 INFO @ Sun, 21 Jun 2020 17:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:36: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 17:18:36: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 17:18:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:36: #2 predicted fragment length is 184 bps INFO @ Sun, 21 Jun 2020 17:18:36: #2 alternative fragment length(s) may be 184 bps INFO @ Sun, 21 Jun 2020 17:18:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.10_model.r WARNING @ Sun, 21 Jun 2020 17:18:36: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:18:36: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Sun, 21 Jun 2020 17:18:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:18:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.05_summits.bed INFO @ Sun, 21 Jun 2020 17:18:40: Done! pass1 - making usageList (342 chroms): 2 millis pass2 - checking and writing primary data (3689 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:45: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:18:56: 9000000 INFO @ Sun, 21 Jun 2020 17:18:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:07: 10000000 INFO @ Sun, 21 Jun 2020 17:19:08: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 17:19:08: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 17:19:08: #1 total tags in treatment: 10102372 INFO @ Sun, 21 Jun 2020 17:19:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:08: #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 17:19:09: #1 tags after filtering in treatment: 10102356 INFO @ Sun, 21 Jun 2020 17:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:09: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 17:19:09: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:09: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:09: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:09: #2 predicted fragment length is 184 bps INFO @ Sun, 21 Jun 2020 17:19:09: #2 alternative fragment length(s) may be 184 bps INFO @ Sun, 21 Jun 2020 17:19:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.20_model.r WARNING @ Sun, 21 Jun 2020 17:19:09: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:19:09: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Sun, 21 Jun 2020 17:19:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:19:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.10_summits.bed INFO @ Sun, 21 Jun 2020 17:19:11: Done! pass1 - making usageList (217 chroms): 1 millis pass2 - checking and writing primary data (1389 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:19:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX059817/SRX059817.20_summits.bed INFO @ Sun, 21 Jun 2020 17:19:48: Done! pass1 - making usageList (107 chroms): 2 millis pass2 - checking and writing primary data (288 records, 4 fields): 5 millis CompletedMACS2peakCalling