Job ID = 6455629 SRX = SRX287941 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:09:51 prefetch.2.10.7: 1) Downloading 'SRR870130'... 2020-06-21T10:09:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:12:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:12:40 prefetch.2.10.7: 1) 'SRR870130' was downloaded successfully Read 18953572 spots for SRR870130/SRR870130.sra Written 18953572 spots for SRR870130/SRR870130.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: 00:06:06 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 1311836 (6.92%) aligned 0 times 11692994 (61.69%) aligned exactly 1 time 5948742 (31.39%) aligned >1 times 93.08% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 3506028 / 17641736 = 0.1987 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 19:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.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 19:24:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:18: 1000000 INFO @ Sun, 21 Jun 2020 19:24:23: 2000000 INFO @ Sun, 21 Jun 2020 19:24:29: 3000000 INFO @ Sun, 21 Jun 2020 19:24:34: 4000000 INFO @ Sun, 21 Jun 2020 19:24:39: 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 19:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.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 19:24:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:45: 6000000 INFO @ Sun, 21 Jun 2020 19:24:48: 1000000 INFO @ Sun, 21 Jun 2020 19:24:50: 7000000 INFO @ Sun, 21 Jun 2020 19:24:53: 2000000 INFO @ Sun, 21 Jun 2020 19:24:56: 8000000 INFO @ Sun, 21 Jun 2020 19:24:59: 3000000 INFO @ Sun, 21 Jun 2020 19:25:01: 9000000 INFO @ Sun, 21 Jun 2020 19:25:04: 4000000 INFO @ Sun, 21 Jun 2020 19:25:07: 10000000 INFO @ Sun, 21 Jun 2020 19:25:09: 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 19:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.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 19:25:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:12: 11000000 INFO @ Sun, 21 Jun 2020 19:25:15: 6000000 INFO @ Sun, 21 Jun 2020 19:25:18: 1000000 INFO @ Sun, 21 Jun 2020 19:25:18: 12000000 INFO @ Sun, 21 Jun 2020 19:25:20: 7000000 INFO @ Sun, 21 Jun 2020 19:25:23: 2000000 INFO @ Sun, 21 Jun 2020 19:25:24: 13000000 INFO @ Sun, 21 Jun 2020 19:25:26: 8000000 INFO @ Sun, 21 Jun 2020 19:25:29: 3000000 INFO @ Sun, 21 Jun 2020 19:25:29: 14000000 INFO @ Sun, 21 Jun 2020 19:25:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:30: #1 total tags in treatment: 14135708 INFO @ Sun, 21 Jun 2020 19:25:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:30: #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 19:25:31: #1 tags after filtering in treatment: 14135708 INFO @ Sun, 21 Jun 2020 19:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:31: 9000000 INFO @ Sun, 21 Jun 2020 19:25:32: #2 number of paired peaks: 690 WARNING @ Sun, 21 Jun 2020 19:25:32: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:32: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:25:32: #2 alternative fragment length(s) may be 3,41,571 bps INFO @ Sun, 21 Jun 2020 19:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.05_model.r WARNING @ Sun, 21 Jun 2020 19:25:32: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:32: #2 You may need to consider one of the other alternative d(s): 3,41,571 WARNING @ Sun, 21 Jun 2020 19:25:32: #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 19:25:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:34: 4000000 INFO @ Sun, 21 Jun 2020 19:25:37: 10000000 INFO @ Sun, 21 Jun 2020 19:25:40: 5000000 INFO @ Sun, 21 Jun 2020 19:25:42: 11000000 INFO @ Sun, 21 Jun 2020 19:25:45: 6000000 INFO @ Sun, 21 Jun 2020 19:25:48: 12000000 INFO @ Sun, 21 Jun 2020 19:25:50: 7000000 INFO @ Sun, 21 Jun 2020 19:25:53: 13000000 INFO @ Sun, 21 Jun 2020 19:25:56: 8000000 INFO @ Sun, 21 Jun 2020 19:25:59: 14000000 INFO @ Sun, 21 Jun 2020 19:25:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:00: #1 total tags in treatment: 14135708 INFO @ Sun, 21 Jun 2020 19:26:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:00: #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 19:26:00: #1 tags after filtering in treatment: 14135708 INFO @ Sun, 21 Jun 2020 19:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:01: #2 number of paired peaks: 690 WARNING @ Sun, 21 Jun 2020 19:26:01: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:01: 9000000 INFO @ Sun, 21 Jun 2020 19:26:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:01: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:26:01: #2 alternative fragment length(s) may be 3,41,571 bps INFO @ Sun, 21 Jun 2020 19:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.10_model.r WARNING @ Sun, 21 Jun 2020 19:26:01: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:01: #2 You may need to consider one of the other alternative d(s): 3,41,571 WARNING @ Sun, 21 Jun 2020 19:26:01: #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 19:26:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:07: 10000000 INFO @ Sun, 21 Jun 2020 19:26:12: 11000000 INFO @ Sun, 21 Jun 2020 19:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:14: Done! pass1 - making usageList (619 chroms): 1 millis pass2 - checking and writing primary data (2334 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:18: 12000000 INFO @ Sun, 21 Jun 2020 19:26:23: 13000000 INFO @ Sun, 21 Jun 2020 19:26:28: 14000000 INFO @ Sun, 21 Jun 2020 19:26:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:29: #1 total tags in treatment: 14135708 INFO @ Sun, 21 Jun 2020 19:26:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:29: #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 19:26:30: #1 tags after filtering in treatment: 14135708 INFO @ Sun, 21 Jun 2020 19:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:31: #2 number of paired peaks: 690 WARNING @ Sun, 21 Jun 2020 19:26:31: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:31: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:26:31: #2 alternative fragment length(s) may be 3,41,571 bps INFO @ Sun, 21 Jun 2020 19:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.20_model.r WARNING @ Sun, 21 Jun 2020 19:26:31: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:31: #2 You may need to consider one of the other alternative d(s): 3,41,571 WARNING @ Sun, 21 Jun 2020 19:26:31: #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 19:26:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.10_summits.bed INFO @ Sun, 21 Jun 2020 19:26:42: Done! pass1 - making usageList (522 chroms): 1 millis pass2 - checking and writing primary data (1982 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:26:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287941/SRX287941.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:11: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (860 records, 4 fields): 10 millis CompletedMACS2peakCalling