Job ID = 6452833 SRX = SRX041390 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:56:30 prefetch.2.10.7: 1) Downloading 'SRR099121'... 2020-06-21T07:56:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:58:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:58:40 prefetch.2.10.7: 'SRR099121' is valid 2020-06-21T07:58:40 prefetch.2.10.7: 1) 'SRR099121' was downloaded successfully Read 19342059 spots for SRR099121/SRR099121.sra Written 19342059 spots for SRR099121/SRR099121.sra 2020-06-21T07:59:41 prefetch.2.10.7: 1) Downloading 'SRR099122'... 2020-06-21T07:59:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:02:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:02:18 prefetch.2.10.7: 'SRR099122' is valid 2020-06-21T08:02:18 prefetch.2.10.7: 1) 'SRR099122' was downloaded successfully Read 16502674 spots for SRR099122/SRR099122.sra Written 16502674 spots for SRR099122/SRR099122.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: 00:09:39 35844733 reads; of these: 35844733 (100.00%) were unpaired; of these: 1671385 (4.66%) aligned 0 times 21784031 (60.77%) aligned exactly 1 time 12389317 (34.56%) aligned >1 times 95.34% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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] 9937274 / 34173348 = 0.2908 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 17:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.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 17:19:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:19:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:19:58: 1000000 INFO @ Sun, 21 Jun 2020 17:20:04: 2000000 INFO @ Sun, 21 Jun 2020 17:20:09: 3000000 INFO @ Sun, 21 Jun 2020 17:20:15: 4000000 INFO @ Sun, 21 Jun 2020 17:20:20: 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 17:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.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 17:20:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:26: 6000000 INFO @ Sun, 21 Jun 2020 17:20:28: 1000000 INFO @ Sun, 21 Jun 2020 17:20:32: 7000000 INFO @ Sun, 21 Jun 2020 17:20:34: 2000000 INFO @ Sun, 21 Jun 2020 17:20:37: 8000000 INFO @ Sun, 21 Jun 2020 17:20:39: 3000000 INFO @ Sun, 21 Jun 2020 17:20:43: 9000000 INFO @ Sun, 21 Jun 2020 17:20:45: 4000000 INFO @ Sun, 21 Jun 2020 17:20:49: 10000000 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 17:20:51: 5000000 INFO @ Sun, 21 Jun 2020 17:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.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 17:20:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:54: 11000000 INFO @ Sun, 21 Jun 2020 17:20:56: 6000000 INFO @ Sun, 21 Jun 2020 17:20:58: 1000000 INFO @ Sun, 21 Jun 2020 17:21:00: 12000000 INFO @ Sun, 21 Jun 2020 17:21:02: 7000000 INFO @ Sun, 21 Jun 2020 17:21:04: 2000000 INFO @ Sun, 21 Jun 2020 17:21:06: 13000000 INFO @ Sun, 21 Jun 2020 17:21:08: 8000000 INFO @ Sun, 21 Jun 2020 17:21:10: 3000000 INFO @ Sun, 21 Jun 2020 17:21:12: 14000000 INFO @ Sun, 21 Jun 2020 17:21:14: 9000000 INFO @ Sun, 21 Jun 2020 17:21:16: 4000000 INFO @ Sun, 21 Jun 2020 17:21:18: 15000000 INFO @ Sun, 21 Jun 2020 17:21:19: 10000000 INFO @ Sun, 21 Jun 2020 17:21:22: 5000000 INFO @ Sun, 21 Jun 2020 17:21:24: 16000000 INFO @ Sun, 21 Jun 2020 17:21:25: 11000000 INFO @ Sun, 21 Jun 2020 17:21:28: 6000000 INFO @ Sun, 21 Jun 2020 17:21:30: 17000000 INFO @ Sun, 21 Jun 2020 17:21:31: 12000000 INFO @ Sun, 21 Jun 2020 17:21:33: 7000000 INFO @ Sun, 21 Jun 2020 17:21:35: 18000000 INFO @ Sun, 21 Jun 2020 17:21:37: 13000000 INFO @ Sun, 21 Jun 2020 17:21:39: 8000000 INFO @ Sun, 21 Jun 2020 17:21:42: 19000000 INFO @ Sun, 21 Jun 2020 17:21:42: 14000000 INFO @ Sun, 21 Jun 2020 17:21:45: 9000000 INFO @ Sun, 21 Jun 2020 17:21:47: 20000000 INFO @ Sun, 21 Jun 2020 17:21:48: 15000000 INFO @ Sun, 21 Jun 2020 17:21:51: 10000000 INFO @ Sun, 21 Jun 2020 17:21:53: 21000000 INFO @ Sun, 21 Jun 2020 17:21:54: 16000000 INFO @ Sun, 21 Jun 2020 17:21:56: 11000000 INFO @ Sun, 21 Jun 2020 17:21:59: 22000000 INFO @ Sun, 21 Jun 2020 17:21:59: 17000000 INFO @ Sun, 21 Jun 2020 17:22:02: 12000000 INFO @ Sun, 21 Jun 2020 17:22:05: 23000000 INFO @ Sun, 21 Jun 2020 17:22:05: 18000000 INFO @ Sun, 21 Jun 2020 17:22:08: 13000000 INFO @ Sun, 21 Jun 2020 17:22:10: 24000000 INFO @ Sun, 21 Jun 2020 17:22:11: 19000000 INFO @ Sun, 21 Jun 2020 17:22:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:22:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:22:12: #1 total tags in treatment: 24236074 INFO @ Sun, 21 Jun 2020 17:22:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:12: #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 17:22:13: #1 tags after filtering in treatment: 24236073 INFO @ Sun, 21 Jun 2020 17:22:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:13: 14000000 INFO @ Sun, 21 Jun 2020 17:22:14: #2 number of paired peaks: 981 WARNING @ Sun, 21 Jun 2020 17:22:14: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Sun, 21 Jun 2020 17:22:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:14: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 17:22:14: #2 alternative fragment length(s) may be 2,37,81,99 bps INFO @ Sun, 21 Jun 2020 17:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.05_model.r WARNING @ Sun, 21 Jun 2020 17:22:14: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:14: #2 You may need to consider one of the other alternative d(s): 2,37,81,99 WARNING @ Sun, 21 Jun 2020 17:22:14: #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 17:22:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:16: 20000000 INFO @ Sun, 21 Jun 2020 17:22:19: 15000000 INFO @ Sun, 21 Jun 2020 17:22:22: 21000000 INFO @ Sun, 21 Jun 2020 17:22:24: 16000000 INFO @ Sun, 21 Jun 2020 17:22:28: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:22:30: 17000000 INFO @ Sun, 21 Jun 2020 17:22:33: 23000000 INFO @ Sun, 21 Jun 2020 17:22:36: 18000000 INFO @ Sun, 21 Jun 2020 17:22:39: 24000000 INFO @ Sun, 21 Jun 2020 17:22:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:22:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:22:40: #1 total tags in treatment: 24236074 INFO @ Sun, 21 Jun 2020 17:22:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:40: #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 17:22:41: #1 tags after filtering in treatment: 24236073 INFO @ Sun, 21 Jun 2020 17:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:41: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:41: 19000000 INFO @ Sun, 21 Jun 2020 17:22:42: #2 number of paired peaks: 981 WARNING @ Sun, 21 Jun 2020 17:22:42: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Sun, 21 Jun 2020 17:22:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:42: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 17:22:42: #2 alternative fragment length(s) may be 2,37,81,99 bps INFO @ Sun, 21 Jun 2020 17:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.10_model.r WARNING @ Sun, 21 Jun 2020 17:22:42: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:42: #2 You may need to consider one of the other alternative d(s): 2,37,81,99 WARNING @ Sun, 21 Jun 2020 17:22:42: #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 17:22:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:46: 20000000 INFO @ Sun, 21 Jun 2020 17:22:51: 21000000 INFO @ Sun, 21 Jun 2020 17:22:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:56: 22000000 INFO @ Sun, 21 Jun 2020 17:23:01: 23000000 INFO @ Sun, 21 Jun 2020 17:23:06: 24000000 INFO @ Sun, 21 Jun 2020 17:23:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:23:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:23:08: #1 total tags in treatment: 24236074 INFO @ Sun, 21 Jun 2020 17:23:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:08: #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 17:23:08: #1 tags after filtering in treatment: 24236073 INFO @ Sun, 21 Jun 2020 17:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:08: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:10: #2 number of paired peaks: 981 WARNING @ Sun, 21 Jun 2020 17:23:10: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Sun, 21 Jun 2020 17:23:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:10: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 17:23:10: #2 alternative fragment length(s) may be 2,37,81,99 bps INFO @ Sun, 21 Jun 2020 17:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.20_model.r WARNING @ Sun, 21 Jun 2020 17:23:10: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:23:10: #2 You may need to consider one of the other alternative d(s): 2,37,81,99 WARNING @ Sun, 21 Jun 2020 17:23:10: #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 17:23:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:18: Done! pass1 - making usageList (910 chroms): 2 millis pass2 - checking and writing primary data (11252 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:23:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.10_summits.bed INFO @ Sun, 21 Jun 2020 17:23:44: Done! pass1 - making usageList (711 chroms): 1 millis pass2 - checking and writing primary data (3990 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041390/SRX041390.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:13: Done! pass1 - making usageList (464 chroms): 1 millis pass2 - checking and writing primary data (1541 records, 4 fields): 13 millis CompletedMACS2peakCalling