Job ID = 6455397 SRX = SRX287753 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:51 prefetch.2.10.7: 1) Downloading 'SRR869942'... 2020-06-21T10:15:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:48 prefetch.2.10.7: 1) 'SRR869942' was downloaded successfully Read 16539414 spots for SRR869942/SRR869942.sra Written 16539414 spots for SRR869942/SRR869942.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: 00:05:14 16539414 reads; of these: 16539414 (100.00%) were unpaired; of these: 1026482 (6.21%) aligned 0 times 10370100 (62.70%) aligned exactly 1 time 5142832 (31.09%) aligned >1 times 93.79% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 2539907 / 15512932 = 0.1637 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 19:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.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 19:29:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:07: 1000000 INFO @ Sun, 21 Jun 2020 19:29:13: 2000000 INFO @ Sun, 21 Jun 2020 19:29:19: 3000000 INFO @ Sun, 21 Jun 2020 19:29:24: 4000000 INFO @ Sun, 21 Jun 2020 19:29:30: 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 19:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.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 19:29:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:36: 6000000 INFO @ Sun, 21 Jun 2020 19:29:38: 1000000 INFO @ Sun, 21 Jun 2020 19:29:42: 7000000 INFO @ Sun, 21 Jun 2020 19:29:44: 2000000 INFO @ Sun, 21 Jun 2020 19:29:48: 8000000 INFO @ Sun, 21 Jun 2020 19:29:51: 3000000 INFO @ Sun, 21 Jun 2020 19:29:54: 9000000 INFO @ Sun, 21 Jun 2020 19:29:57: 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 @ Sun, 21 Jun 2020 19:30:00: 10000000 INFO @ Sun, 21 Jun 2020 19:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.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 19:30:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:03: 5000000 INFO @ Sun, 21 Jun 2020 19:30:06: 11000000 INFO @ Sun, 21 Jun 2020 19:30:08: 1000000 INFO @ Sun, 21 Jun 2020 19:30:10: 6000000 INFO @ Sun, 21 Jun 2020 19:30:13: 12000000 INFO @ Sun, 21 Jun 2020 19:30:15: 2000000 INFO @ Sun, 21 Jun 2020 19:30:16: 7000000 INFO @ Sun, 21 Jun 2020 19:30:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:19: #1 total tags in treatment: 12973025 INFO @ Sun, 21 Jun 2020 19:30:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:19: #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 19:30:20: #1 tags after filtering in treatment: 12973025 INFO @ Sun, 21 Jun 2020 19:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:21: #2 number of paired peaks: 555 WARNING @ Sun, 21 Jun 2020 19:30:21: Fewer paired peaks (555) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 555 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:21: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:30:21: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:30:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.05_model.r WARNING @ Sun, 21 Jun 2020 19:30:21: #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 19:30:21: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:30:21: #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 19:30:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:22: 3000000 INFO @ Sun, 21 Jun 2020 19:30:23: 8000000 INFO @ Sun, 21 Jun 2020 19:30:28: 4000000 INFO @ Sun, 21 Jun 2020 19:30:29: 9000000 INFO @ Sun, 21 Jun 2020 19:30:34: 5000000 INFO @ Sun, 21 Jun 2020 19:30:35: 10000000 INFO @ Sun, 21 Jun 2020 19:30:41: 6000000 INFO @ Sun, 21 Jun 2020 19:30:42: 11000000 INFO @ Sun, 21 Jun 2020 19:30:48: 7000000 INFO @ Sun, 21 Jun 2020 19:30:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:48: 12000000 INFO @ Sun, 21 Jun 2020 19:30:55: 8000000 INFO @ Sun, 21 Jun 2020 19:30:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:55: #1 total tags in treatment: 12973025 INFO @ Sun, 21 Jun 2020 19:30:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:55: #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 19:30:56: #1 tags after filtering in treatment: 12973025 INFO @ Sun, 21 Jun 2020 19:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:57: #2 number of paired peaks: 555 WARNING @ Sun, 21 Jun 2020 19:30:57: Fewer paired peaks (555) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 555 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:57: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:30:57: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.10_model.r WARNING @ Sun, 21 Jun 2020 19:30:57: #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 19:30:57: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:30:57: #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 19:30:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:01: 9000000 INFO @ Sun, 21 Jun 2020 19:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:01: Done! pass1 - making usageList (619 chroms): 1 millis pass2 - checking and writing primary data (2461 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:31:07: 10000000 INFO @ Sun, 21 Jun 2020 19:31:13: 11000000 INFO @ Sun, 21 Jun 2020 19:31:19: 12000000 INFO @ Sun, 21 Jun 2020 19:31:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:24: #1 total tags in treatment: 12973025 INFO @ Sun, 21 Jun 2020 19:31:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:24: #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 19:31:25: #1 tags after filtering in treatment: 12973025 INFO @ Sun, 21 Jun 2020 19:31:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:26: #2 number of paired peaks: 555 WARNING @ Sun, 21 Jun 2020 19:31:26: Fewer paired peaks (555) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 555 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:26: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:31:26: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.20_model.r WARNING @ Sun, 21 Jun 2020 19:31:26: #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 19:31:26: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:31:26: #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 19:31:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:36: Done! pass1 - making usageList (509 chroms): 2 millis pass2 - checking and writing primary data (1832 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287753/SRX287753.20_summits.bed INFO @ Sun, 21 Jun 2020 19:32:05: Done! pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 10 millis CompletedMACS2peakCalling