Job ID = 6458877 SRX = SRX5717046 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:25 prefetch.2.10.7: 1) Downloading 'SRR8936407'... 2020-06-21T12:49:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:52:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:52:17 prefetch.2.10.7: 1) 'SRR8936407' was downloaded successfully Read 24552942 spots for SRR8936407/SRR8936407.sra Written 24552942 spots for SRR8936407/SRR8936407.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: 00:05:40 24552942 reads; of these: 24552942 (100.00%) were unpaired; of these: 2358632 (9.61%) aligned 0 times 17549474 (71.48%) aligned exactly 1 time 4644836 (18.92%) aligned >1 times 90.39% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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_sort_core] merging from 12 files... [bam_rmdupse_core] 6878521 / 22194310 = 0.3099 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 22:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.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 22:03:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:39: 1000000 INFO @ Sun, 21 Jun 2020 22:03:44: 2000000 INFO @ Sun, 21 Jun 2020 22:03:49: 3000000 INFO @ Sun, 21 Jun 2020 22:03:53: 4000000 INFO @ Sun, 21 Jun 2020 22:03:58: 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 22:04:03: 6000000 INFO @ Sun, 21 Jun 2020 22:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.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 22:04:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:08: 7000000 INFO @ Sun, 21 Jun 2020 22:04:10: 1000000 INFO @ Sun, 21 Jun 2020 22:04:13: 8000000 INFO @ Sun, 21 Jun 2020 22:04:16: 2000000 INFO @ Sun, 21 Jun 2020 22:04:18: 9000000 INFO @ Sun, 21 Jun 2020 22:04:21: 3000000 INFO @ Sun, 21 Jun 2020 22:04:23: 10000000 INFO @ Sun, 21 Jun 2020 22:04:27: 4000000 INFO @ Sun, 21 Jun 2020 22:04:28: 11000000 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 22:04:33: 5000000 INFO @ Sun, 21 Jun 2020 22:04:33: 12000000 INFO @ Sun, 21 Jun 2020 22:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.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 22:04:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:39: 6000000 INFO @ Sun, 21 Jun 2020 22:04:39: 13000000 INFO @ Sun, 21 Jun 2020 22:04:39: 1000000 INFO @ Sun, 21 Jun 2020 22:04:44: 14000000 INFO @ Sun, 21 Jun 2020 22:04:44: 7000000 INFO @ Sun, 21 Jun 2020 22:04:45: 2000000 INFO @ Sun, 21 Jun 2020 22:04:49: 15000000 INFO @ Sun, 21 Jun 2020 22:04:50: 3000000 INFO @ Sun, 21 Jun 2020 22:04:50: 8000000 INFO @ Sun, 21 Jun 2020 22:04:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:04:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:04:51: #1 total tags in treatment: 15315789 INFO @ Sun, 21 Jun 2020 22:04:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:51: #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 22:04:51: #1 tags after filtering in treatment: 15315702 INFO @ Sun, 21 Jun 2020 22:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:52: #2 number of paired peaks: 220 WARNING @ Sun, 21 Jun 2020 22:04:52: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:53: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:04:53: #2 alternative fragment length(s) may be 47,104,108,141,189,215,227,253,285,399,446,464 bps INFO @ Sun, 21 Jun 2020 22:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:53: #2 You may need to consider one of the other alternative d(s): 47,104,108,141,189,215,227,253,285,399,446,464 WARNING @ Sun, 21 Jun 2020 22:04:53: #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 22:04:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:55: 4000000 INFO @ Sun, 21 Jun 2020 22:04:56: 9000000 INFO @ Sun, 21 Jun 2020 22:05:00: 5000000 INFO @ Sun, 21 Jun 2020 22:05:02: 10000000 INFO @ Sun, 21 Jun 2020 22:05:05: 6000000 INFO @ Sun, 21 Jun 2020 22:05:07: 11000000 INFO @ Sun, 21 Jun 2020 22:05:11: 7000000 INFO @ Sun, 21 Jun 2020 22:05:13: 12000000 INFO @ Sun, 21 Jun 2020 22:05:16: 8000000 INFO @ Sun, 21 Jun 2020 22:05:19: 13000000 INFO @ Sun, 21 Jun 2020 22:05:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:21: 9000000 INFO @ Sun, 21 Jun 2020 22:05:25: 14000000 INFO @ Sun, 21 Jun 2020 22:05:26: 10000000 INFO @ Sun, 21 Jun 2020 22:05:30: 15000000 INFO @ Sun, 21 Jun 2020 22:05:31: 11000000 INFO @ Sun, 21 Jun 2020 22:05:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:05:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:05:32: #1 total tags in treatment: 15315789 INFO @ Sun, 21 Jun 2020 22:05:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:32: #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 22:05:33: #1 tags after filtering in treatment: 15315702 INFO @ Sun, 21 Jun 2020 22:05:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:33: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (889 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:34: #2 number of paired peaks: 220 WARNING @ Sun, 21 Jun 2020 22:05:34: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:34: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:05:34: #2 alternative fragment length(s) may be 47,104,108,141,189,215,227,253,285,399,446,464 bps INFO @ Sun, 21 Jun 2020 22:05:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.10_model.r WARNING @ Sun, 21 Jun 2020 22:05:34: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:34: #2 You may need to consider one of the other alternative d(s): 47,104,108,141,189,215,227,253,285,399,446,464 WARNING @ Sun, 21 Jun 2020 22:05:34: #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 22:05:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:36: 12000000 INFO @ Sun, 21 Jun 2020 22:05:42: 13000000 INFO @ Sun, 21 Jun 2020 22:05:46: 14000000 INFO @ Sun, 21 Jun 2020 22:05:51: 15000000 INFO @ Sun, 21 Jun 2020 22:05:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:05:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:05:53: #1 total tags in treatment: 15315789 INFO @ Sun, 21 Jun 2020 22:05:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:54: #1 tags after filtering in treatment: 15315702 INFO @ Sun, 21 Jun 2020 22:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:55: #2 number of paired peaks: 220 WARNING @ Sun, 21 Jun 2020 22:05:55: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:55: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:05:55: #2 alternative fragment length(s) may be 47,104,108,141,189,215,227,253,285,399,446,464 bps INFO @ Sun, 21 Jun 2020 22:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:55: #2 You may need to consider one of the other alternative d(s): 47,104,108,141,189,215,227,253,285,399,446,464 WARNING @ Sun, 21 Jun 2020 22:05:55: #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 22:05:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.10_summits.bed INFO @ Sun, 21 Jun 2020 22:06:15: Done! pass1 - making usageList (96 chroms): 0 millis pass2 - checking and writing primary data (267 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717046/SRX5717046.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:36: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (52 records, 4 fields): 2 millis CompletedMACS2peakCalling