Job ID = 6527936 SRX = SRX331370 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:41:11 prefetch.2.10.7: 1) Downloading 'SRR947607'... 2020-06-29T13:41:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:46:02 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:46:02 prefetch.2.10.7: 1) 'SRR947607' was downloaded successfully Read 21559305 spots for SRR947607/SRR947607.sra Written 21559305 spots for SRR947607/SRR947607.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: 00:07:04 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1335760 (6.20%) aligned 0 times 15428616 (71.56%) aligned exactly 1 time 4794929 (22.24%) aligned >1 times 93.80% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1889996 / 20223545 = 0.0935 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 @ Mon, 29 Jun 2020 23:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.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 @ Mon, 29 Jun 2020 23:07:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:07:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:07:32: 1000000 INFO @ Mon, 29 Jun 2020 23:07:39: 2000000 INFO @ Mon, 29 Jun 2020 23:07:45: 3000000 INFO @ Mon, 29 Jun 2020 23:07:52: 4000000 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 @ Mon, 29 Jun 2020 23:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.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 @ Mon, 29 Jun 2020 23:07:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:07:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:07:58: 5000000 INFO @ Mon, 29 Jun 2020 23:08:02: 1000000 INFO @ Mon, 29 Jun 2020 23:08:05: 6000000 INFO @ Mon, 29 Jun 2020 23:08:09: 2000000 INFO @ Mon, 29 Jun 2020 23:08:11: 7000000 INFO @ Mon, 29 Jun 2020 23:08:15: 3000000 INFO @ Mon, 29 Jun 2020 23:08:18: 8000000 INFO @ Mon, 29 Jun 2020 23:08:21: 4000000 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 @ Mon, 29 Jun 2020 23:08:24: 9000000 INFO @ Mon, 29 Jun 2020 23:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.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 @ Mon, 29 Jun 2020 23:08:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:28: 5000000 INFO @ Mon, 29 Jun 2020 23:08:31: 10000000 INFO @ Mon, 29 Jun 2020 23:08:33: 1000000 INFO @ Mon, 29 Jun 2020 23:08:35: 6000000 INFO @ Mon, 29 Jun 2020 23:08:37: 11000000 INFO @ Mon, 29 Jun 2020 23:08:41: 2000000 INFO @ Mon, 29 Jun 2020 23:08:42: 7000000 INFO @ Mon, 29 Jun 2020 23:08:44: 12000000 INFO @ Mon, 29 Jun 2020 23:08:48: 3000000 INFO @ Mon, 29 Jun 2020 23:08:50: 8000000 INFO @ Mon, 29 Jun 2020 23:08:50: 13000000 INFO @ Mon, 29 Jun 2020 23:08:56: 4000000 INFO @ Mon, 29 Jun 2020 23:08:57: 9000000 INFO @ Mon, 29 Jun 2020 23:08:57: 14000000 INFO @ Mon, 29 Jun 2020 23:09:04: 5000000 INFO @ Mon, 29 Jun 2020 23:09:04: 15000000 INFO @ Mon, 29 Jun 2020 23:09:04: 10000000 INFO @ Mon, 29 Jun 2020 23:09:10: 16000000 INFO @ Mon, 29 Jun 2020 23:09:11: 11000000 INFO @ Mon, 29 Jun 2020 23:09:12: 6000000 INFO @ Mon, 29 Jun 2020 23:09:17: 17000000 INFO @ Mon, 29 Jun 2020 23:09:19: 12000000 INFO @ Mon, 29 Jun 2020 23:09:19: 7000000 INFO @ Mon, 29 Jun 2020 23:09:23: 18000000 INFO @ Mon, 29 Jun 2020 23:09:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:09:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:09:26: #1 total tags in treatment: 18333549 INFO @ Mon, 29 Jun 2020 23:09:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:09:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:09:26: #1 tags after filtering in treatment: 18333549 INFO @ Mon, 29 Jun 2020 23:09:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:09:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:09:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:09:26: 13000000 INFO @ Mon, 29 Jun 2020 23:09:27: 8000000 INFO @ Mon, 29 Jun 2020 23:09:27: #2 number of paired peaks: 148 WARNING @ Mon, 29 Jun 2020 23:09:27: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Mon, 29 Jun 2020 23:09:27: start model_add_line... INFO @ Mon, 29 Jun 2020 23:09:27: start X-correlation... INFO @ Mon, 29 Jun 2020 23:09:27: end of X-cor INFO @ Mon, 29 Jun 2020 23:09:27: #2 finished! INFO @ Mon, 29 Jun 2020 23:09:27: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:09:27: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.05_model.r WARNING @ Mon, 29 Jun 2020 23:09:27: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:09:27: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:09:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:09:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:09:34: 14000000 INFO @ Mon, 29 Jun 2020 23:09:35: 9000000 INFO @ Mon, 29 Jun 2020 23:09:42: 15000000 INFO @ Mon, 29 Jun 2020 23:09:42: 10000000 INFO @ Mon, 29 Jun 2020 23:09:49: 16000000 INFO @ Mon, 29 Jun 2020 23:09:50: 11000000 INFO @ Mon, 29 Jun 2020 23:09:57: 17000000 INFO @ Mon, 29 Jun 2020 23:09:57: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:09:58: 12000000 INFO @ Mon, 29 Jun 2020 23:10:04: 18000000 INFO @ Mon, 29 Jun 2020 23:10:05: 13000000 INFO @ Mon, 29 Jun 2020 23:10:07: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:07: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:07: #1 total tags in treatment: 18333549 INFO @ Mon, 29 Jun 2020 23:10:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:10:07: #1 tags after filtering in treatment: 18333549 INFO @ Mon, 29 Jun 2020 23:10:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:07: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:08: #2 number of paired peaks: 148 WARNING @ Mon, 29 Jun 2020 23:10:08: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:08: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:08: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:08: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:08: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:08: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:10:08: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.10_model.r WARNING @ Mon, 29 Jun 2020 23:10:08: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:08: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:10:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:10:08: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:10:12: 14000000 INFO @ Mon, 29 Jun 2020 23:10:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.05_summits.bed INFO @ Mon, 29 Jun 2020 23:10:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1975 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:10:19: 15000000 INFO @ Mon, 29 Jun 2020 23:10:26: 16000000 INFO @ Mon, 29 Jun 2020 23:10:33: 17000000 INFO @ Mon, 29 Jun 2020 23:10:39: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:10:40: 18000000 INFO @ Mon, 29 Jun 2020 23:10:42: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:42: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:42: #1 total tags in treatment: 18333549 INFO @ Mon, 29 Jun 2020 23:10:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:10:42: #1 tags after filtering in treatment: 18333549 INFO @ Mon, 29 Jun 2020 23:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:42: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:42: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:44: #2 number of paired peaks: 148 WARNING @ Mon, 29 Jun 2020 23:10:44: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:44: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:44: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:44: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:44: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:44: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:10:44: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:10:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.20_model.r WARNING @ Mon, 29 Jun 2020 23:10:44: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:44: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:10:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:10:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.10_summits.bed INFO @ Mon, 29 Jun 2020 23:10:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1622 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:11:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331370/SRX331370.20_summits.bed INFO @ Mon, 29 Jun 2020 23:11:29: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1077 records, 4 fields): 4 millis CompletedMACS2peakCalling