Job ID = 6455250 SRX = SRX287592 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:06:40 prefetch.2.10.7: 1) Downloading 'SRR869735'... 2020-06-21T10:06:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:15 prefetch.2.10.7: 1) 'SRR869735' was downloaded successfully Read 21566409 spots for SRR869735/SRR869735.sra Written 21566409 spots for SRR869735/SRR869735.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: 00:06:19 21566409 reads; of these: 21566409 (100.00%) were unpaired; of these: 1217073 (5.64%) aligned 0 times 14708227 (68.20%) aligned exactly 1 time 5641109 (26.16%) aligned >1 times 94.36% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 3675674 / 20349336 = 0.1806 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 19:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.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 19:23:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:52: 1000000 INFO @ Sun, 21 Jun 2020 19:23:57: 2000000 INFO @ Sun, 21 Jun 2020 19:24:02: 3000000 INFO @ Sun, 21 Jun 2020 19:24:07: 4000000 INFO @ Sun, 21 Jun 2020 19:24:12: 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 19:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.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 19:24:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:18: 6000000 INFO @ Sun, 21 Jun 2020 19:24:23: 1000000 INFO @ Sun, 21 Jun 2020 19:24:23: 7000000 INFO @ Sun, 21 Jun 2020 19:24:29: 8000000 INFO @ Sun, 21 Jun 2020 19:24:30: 2000000 INFO @ Sun, 21 Jun 2020 19:24:35: 9000000 INFO @ Sun, 21 Jun 2020 19:24:36: 3000000 INFO @ Sun, 21 Jun 2020 19:24:41: 10000000 INFO @ Sun, 21 Jun 2020 19:24:43: 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 19:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.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 19:24:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:47: 11000000 INFO @ Sun, 21 Jun 2020 19:24:50: 5000000 INFO @ Sun, 21 Jun 2020 19:24:52: 1000000 INFO @ Sun, 21 Jun 2020 19:24:53: 12000000 INFO @ Sun, 21 Jun 2020 19:24:56: 6000000 INFO @ Sun, 21 Jun 2020 19:24:58: 2000000 INFO @ Sun, 21 Jun 2020 19:24:58: 13000000 INFO @ Sun, 21 Jun 2020 19:25:03: 7000000 INFO @ Sun, 21 Jun 2020 19:25:04: 3000000 INFO @ Sun, 21 Jun 2020 19:25:05: 14000000 INFO @ Sun, 21 Jun 2020 19:25:10: 8000000 INFO @ Sun, 21 Jun 2020 19:25:10: 4000000 INFO @ Sun, 21 Jun 2020 19:25:10: 15000000 INFO @ Sun, 21 Jun 2020 19:25:16: 5000000 INFO @ Sun, 21 Jun 2020 19:25:16: 9000000 INFO @ Sun, 21 Jun 2020 19:25:16: 16000000 INFO @ Sun, 21 Jun 2020 19:25:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:20: #1 total tags in treatment: 16673662 INFO @ Sun, 21 Jun 2020 19:25:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:20: #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 19:25:21: #1 tags after filtering in treatment: 16673662 INFO @ Sun, 21 Jun 2020 19:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:22: 6000000 INFO @ Sun, 21 Jun 2020 19:25:22: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 19:25:22: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:22: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:25:22: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.05_model.r WARNING @ Sun, 21 Jun 2020 19:25:22: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:22: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:25:22: #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 19:25:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:23: 10000000 INFO @ Sun, 21 Jun 2020 19:25:27: 7000000 INFO @ Sun, 21 Jun 2020 19:25:29: 11000000 INFO @ Sun, 21 Jun 2020 19:25:33: 8000000 INFO @ Sun, 21 Jun 2020 19:25:36: 12000000 INFO @ Sun, 21 Jun 2020 19:25:39: 9000000 INFO @ Sun, 21 Jun 2020 19:25:43: 13000000 INFO @ Sun, 21 Jun 2020 19:25:45: 10000000 INFO @ Sun, 21 Jun 2020 19:25:49: 14000000 INFO @ Sun, 21 Jun 2020 19:25:50: 11000000 INFO @ Sun, 21 Jun 2020 19:25:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:55: 15000000 INFO @ Sun, 21 Jun 2020 19:25:56: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:01: 16000000 INFO @ Sun, 21 Jun 2020 19:26:02: 13000000 INFO @ Sun, 21 Jun 2020 19:26:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:05: #1 total tags in treatment: 16673662 INFO @ Sun, 21 Jun 2020 19:26:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:05: #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 19:26:06: #1 tags after filtering in treatment: 16673662 INFO @ Sun, 21 Jun 2020 19:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:07: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 19:26:07: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:07: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:26:07: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.10_model.r WARNING @ Sun, 21 Jun 2020 19:26:07: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:07: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:26:07: #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 19:26:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:07: Done! pass1 - making usageList (669 chroms): 2 millis pass2 - checking and writing primary data (2875 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:08: 14000000 INFO @ Sun, 21 Jun 2020 19:26:13: 15000000 INFO @ Sun, 21 Jun 2020 19:26:19: 16000000 INFO @ Sun, 21 Jun 2020 19:26:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:23: #1 total tags in treatment: 16673662 INFO @ Sun, 21 Jun 2020 19:26:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:23: #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 19:26:23: #1 tags after filtering in treatment: 16673662 INFO @ Sun, 21 Jun 2020 19:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:25: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 19:26:25: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:25: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:26:25: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 21 Jun 2020 19:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.20_model.r WARNING @ Sun, 21 Jun 2020 19:26:25: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:25: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 21 Jun 2020 19:26:25: #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 19:26:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:26:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.10_summits.bed INFO @ Sun, 21 Jun 2020 19:26:52: Done! pass1 - making usageList (570 chroms): 1 millis pass2 - checking and writing primary data (2162 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287592/SRX287592.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:08: Done! pass1 - making usageList (431 chroms): 1 millis pass2 - checking and writing primary data (1297 records, 4 fields): 12 millis CompletedMACS2peakCalling