Job ID = 6455364 SRX = SRX287729 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:01:14 prefetch.2.10.7: 1) Downloading 'SRR869918'... 2020-06-21T10:01:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:04 prefetch.2.10.7: 1) 'SRR869918' was downloaded successfully Read 18493128 spots for SRR869918/SRR869918.sra Written 18493128 spots for SRR869918/SRR869918.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: 00:05:09 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1283987 (6.94%) aligned 0 times 13227036 (71.52%) aligned exactly 1 time 3982105 (21.53%) aligned >1 times 93.06% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1868544 / 17209141 = 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 19:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.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 19:14:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:06: 1000000 INFO @ Sun, 21 Jun 2020 19:15:12: 2000000 INFO @ Sun, 21 Jun 2020 19:15:19: 3000000 INFO @ Sun, 21 Jun 2020 19:15:25: 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 19:15:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.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 19:15:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:32: 5000000 INFO @ Sun, 21 Jun 2020 19:15:36: 1000000 INFO @ Sun, 21 Jun 2020 19:15:38: 6000000 INFO @ Sun, 21 Jun 2020 19:15:43: 2000000 INFO @ Sun, 21 Jun 2020 19:15:45: 7000000 INFO @ Sun, 21 Jun 2020 19:15:50: 3000000 INFO @ Sun, 21 Jun 2020 19:15:52: 8000000 INFO @ Sun, 21 Jun 2020 19:15:56: 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 19:15:59: 9000000 INFO @ Sun, 21 Jun 2020 19:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.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 19:15:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:03: 5000000 INFO @ Sun, 21 Jun 2020 19:16:05: 10000000 INFO @ Sun, 21 Jun 2020 19:16:06: 1000000 INFO @ Sun, 21 Jun 2020 19:16:10: 6000000 INFO @ Sun, 21 Jun 2020 19:16:12: 2000000 INFO @ Sun, 21 Jun 2020 19:16:12: 11000000 INFO @ Sun, 21 Jun 2020 19:16:17: 7000000 INFO @ Sun, 21 Jun 2020 19:16:18: 3000000 INFO @ Sun, 21 Jun 2020 19:16:19: 12000000 INFO @ Sun, 21 Jun 2020 19:16:24: 8000000 INFO @ Sun, 21 Jun 2020 19:16:25: 4000000 INFO @ Sun, 21 Jun 2020 19:16:26: 13000000 INFO @ Sun, 21 Jun 2020 19:16:31: 9000000 INFO @ Sun, 21 Jun 2020 19:16:31: 5000000 INFO @ Sun, 21 Jun 2020 19:16:33: 14000000 INFO @ Sun, 21 Jun 2020 19:16:38: 6000000 INFO @ Sun, 21 Jun 2020 19:16:38: 10000000 INFO @ Sun, 21 Jun 2020 19:16:40: 15000000 INFO @ Sun, 21 Jun 2020 19:16:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:42: #1 total tags in treatment: 15340597 INFO @ Sun, 21 Jun 2020 19:16:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:42: #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 19:16:43: #1 tags after filtering in treatment: 15340596 INFO @ Sun, 21 Jun 2020 19:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:44: #2 number of paired peaks: 295 WARNING @ Sun, 21 Jun 2020 19:16:44: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:44: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:16:44: #2 alternative fragment length(s) may be 3,41,527 bps INFO @ Sun, 21 Jun 2020 19:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.05_model.r WARNING @ Sun, 21 Jun 2020 19:16:44: #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 19:16:44: #2 You may need to consider one of the other alternative d(s): 3,41,527 WARNING @ Sun, 21 Jun 2020 19:16:44: #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 19:16:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:44: 7000000 INFO @ Sun, 21 Jun 2020 19:16:45: 11000000 INFO @ Sun, 21 Jun 2020 19:16:50: 8000000 INFO @ Sun, 21 Jun 2020 19:16:53: 12000000 INFO @ Sun, 21 Jun 2020 19:16:56: 9000000 INFO @ Sun, 21 Jun 2020 19:17:00: 13000000 INFO @ Sun, 21 Jun 2020 19:17:03: 10000000 INFO @ Sun, 21 Jun 2020 19:17:07: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:17:09: 11000000 INFO @ Sun, 21 Jun 2020 19:17:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:14: 15000000 INFO @ Sun, 21 Jun 2020 19:17:15: 12000000 INFO @ Sun, 21 Jun 2020 19:17:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:17: #1 total tags in treatment: 15340597 INFO @ Sun, 21 Jun 2020 19:17:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:17: #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 19:17:18: #1 tags after filtering in treatment: 15340596 INFO @ Sun, 21 Jun 2020 19:17:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:19: #2 number of paired peaks: 295 WARNING @ Sun, 21 Jun 2020 19:17:19: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:19: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:17:19: #2 alternative fragment length(s) may be 3,41,527 bps INFO @ Sun, 21 Jun 2020 19:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.10_model.r WARNING @ Sun, 21 Jun 2020 19:17:19: #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 19:17:19: #2 You may need to consider one of the other alternative d(s): 3,41,527 WARNING @ Sun, 21 Jun 2020 19:17:19: #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 19:17:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:22: 13000000 INFO @ Sun, 21 Jun 2020 19:17:27: 14000000 INFO @ Sun, 21 Jun 2020 19:17:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.05_summits.bed INFO @ Sun, 21 Jun 2020 19:17:28: Done! pass1 - making usageList (513 chroms): 1 millis pass2 - checking and writing primary data (2179 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:33: 15000000 INFO @ Sun, 21 Jun 2020 19:17:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:35: #1 total tags in treatment: 15340597 INFO @ Sun, 21 Jun 2020 19:17:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:35: #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 19:17:36: #1 tags after filtering in treatment: 15340596 INFO @ Sun, 21 Jun 2020 19:17:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:37: #2 number of paired peaks: 295 WARNING @ Sun, 21 Jun 2020 19:17:37: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:37: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:17:37: #2 alternative fragment length(s) may be 3,41,527 bps INFO @ Sun, 21 Jun 2020 19:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.20_model.r WARNING @ Sun, 21 Jun 2020 19:17:37: #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 19:17:37: #2 You may need to consider one of the other alternative d(s): 3,41,527 WARNING @ Sun, 21 Jun 2020 19:17:37: #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 19:17:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:17:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.10_summits.bed INFO @ Sun, 21 Jun 2020 19:18:05: Done! pass1 - making usageList (423 chroms): 1 millis pass2 - checking and writing primary data (1342 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287729/SRX287729.20_summits.bed INFO @ Sun, 21 Jun 2020 19:18:23: Done! pass1 - making usageList (200 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 7 millis CompletedMACS2peakCalling