Job ID = 6455460 SRX = SRX287805 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:11:51 prefetch.2.10.7: 1) Downloading 'SRR869994'... 2020-06-21T10:11:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:32 prefetch.2.10.7: 1) 'SRR869994' was downloaded successfully Read 18493128 spots for SRR869994/SRR869994.sra Written 18493128 spots for SRR869994/SRR869994.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 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1283980 (6.94%) aligned 0 times 13226965 (71.52%) aligned exactly 1 time 3982183 (21.53%) aligned >1 times 93.06% 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] 1868806 / 17209148 = 0.1086 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 19:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.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 19:25:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:28: 1000000 INFO @ Sun, 21 Jun 2020 19:25:34: 2000000 INFO @ Sun, 21 Jun 2020 19:25:41: 3000000 INFO @ Sun, 21 Jun 2020 19:25:47: 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 @ Sun, 21 Jun 2020 19:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.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 19:25:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:53: 5000000 INFO @ Sun, 21 Jun 2020 19:25:58: 1000000 INFO @ Sun, 21 Jun 2020 19:26:00: 6000000 INFO @ Sun, 21 Jun 2020 19:26:05: 2000000 INFO @ Sun, 21 Jun 2020 19:26:07: 7000000 INFO @ Sun, 21 Jun 2020 19:26:11: 3000000 INFO @ Sun, 21 Jun 2020 19:26:14: 8000000 INFO @ Sun, 21 Jun 2020 19:26:18: 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 19:26:21: 9000000 INFO @ Sun, 21 Jun 2020 19:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.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 19:26:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:24: 5000000 INFO @ Sun, 21 Jun 2020 19:26:28: 10000000 INFO @ Sun, 21 Jun 2020 19:26:28: 1000000 INFO @ Sun, 21 Jun 2020 19:26:31: 6000000 INFO @ Sun, 21 Jun 2020 19:26:35: 2000000 INFO @ Sun, 21 Jun 2020 19:26:35: 11000000 INFO @ Sun, 21 Jun 2020 19:26:38: 7000000 INFO @ Sun, 21 Jun 2020 19:26:41: 3000000 INFO @ Sun, 21 Jun 2020 19:26:42: 12000000 INFO @ Sun, 21 Jun 2020 19:26:44: 8000000 INFO @ Sun, 21 Jun 2020 19:26:48: 4000000 INFO @ Sun, 21 Jun 2020 19:26:49: 13000000 INFO @ Sun, 21 Jun 2020 19:26:51: 9000000 INFO @ Sun, 21 Jun 2020 19:26:54: 5000000 INFO @ Sun, 21 Jun 2020 19:26:56: 14000000 INFO @ Sun, 21 Jun 2020 19:26:57: 10000000 INFO @ Sun, 21 Jun 2020 19:27:01: 6000000 INFO @ Sun, 21 Jun 2020 19:27:03: 15000000 INFO @ Sun, 21 Jun 2020 19:27:04: 11000000 INFO @ Sun, 21 Jun 2020 19:27:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:06: #1 total tags in treatment: 15340342 INFO @ Sun, 21 Jun 2020 19:27:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:06: #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 19:27:06: #1 tags after filtering in treatment: 15340342 INFO @ Sun, 21 Jun 2020 19:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:07: 7000000 INFO @ Sun, 21 Jun 2020 19:27:07: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 19:27:07: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:07: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:27:07: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sun, 21 Jun 2020 19:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.05_model.r WARNING @ Sun, 21 Jun 2020 19:27:07: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:07: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sun, 21 Jun 2020 19:27:07: #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 19:27:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:10: 12000000 INFO @ Sun, 21 Jun 2020 19:27:13: 8000000 INFO @ Sun, 21 Jun 2020 19:27:17: 13000000 INFO @ Sun, 21 Jun 2020 19:27:20: 9000000 INFO @ Sun, 21 Jun 2020 19:27:23: 14000000 INFO @ Sun, 21 Jun 2020 19:27:26: 10000000 INFO @ Sun, 21 Jun 2020 19:27:30: 15000000 INFO @ Sun, 21 Jun 2020 19:27:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:32: #1 total tags in treatment: 15340342 INFO @ Sun, 21 Jun 2020 19:27:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:32: #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 19:27:32: 11000000 INFO @ Sun, 21 Jun 2020 19:27:32: #1 tags after filtering in treatment: 15340342 INFO @ Sun, 21 Jun 2020 19:27:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:33: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 19:27:33: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:34: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:27:34: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sun, 21 Jun 2020 19:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.10_model.r WARNING @ Sun, 21 Jun 2020 19:27:34: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:34: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sun, 21 Jun 2020 19:27:34: #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 19:27:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:27:44: 13000000 INFO @ Sun, 21 Jun 2020 19:27:50: 14000000 INFO @ Sun, 21 Jun 2020 19:27:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.05_summits.bed INFO @ Sun, 21 Jun 2020 19:27:51: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (2188 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:55: 15000000 INFO @ Sun, 21 Jun 2020 19:27:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:57: #1 total tags in treatment: 15340342 INFO @ Sun, 21 Jun 2020 19:27:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:57: #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 19:27:58: #1 tags after filtering in treatment: 15340342 INFO @ Sun, 21 Jun 2020 19:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:59: #2 number of paired peaks: 285 WARNING @ Sun, 21 Jun 2020 19:27:59: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:59: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:27:59: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sun, 21 Jun 2020 19:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.20_model.r WARNING @ Sun, 21 Jun 2020 19:27:59: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:59: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sun, 21 Jun 2020 19:27:59: #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 19:27:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:17: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1266 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287805/SRX287805.20_summits.bed INFO @ Sun, 21 Jun 2020 19:28:43: Done! pass1 - making usageList (199 chroms): 1 millis pass2 - checking and writing primary data (446 records, 4 fields): 8 millis CompletedMACS2peakCalling