Job ID = 6455876 SRX = SRX3020542 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:26:36 prefetch.2.10.7: 1) Downloading 'SRR5850428'... 2020-06-21T10:26:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:10 prefetch.2.10.7: 'SRR5850428' is valid 2020-06-21T10:27:10 prefetch.2.10.7: 1) 'SRR5850428' was downloaded successfully 2020-06-21T10:27:10 prefetch.2.10.7: 'SRR5850428' has 0 unresolved dependencies Read 6752513 spots for SRR5850428/SRR5850428.sra Written 6752513 spots for SRR5850428/SRR5850428.sra 2020-06-21T10:27:42 prefetch.2.10.7: 1) Downloading 'SRR5850429'... 2020-06-21T10:27:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:50 prefetch.2.10.7: 'SRR5850429' is valid 2020-06-21T10:28:50 prefetch.2.10.7: 1) 'SRR5850429' was downloaded successfully 2020-06-21T10:28:50 prefetch.2.10.7: 'SRR5850429' has 0 unresolved dependencies Read 6720881 spots for SRR5850429/SRR5850429.sra Written 6720881 spots for SRR5850429/SRR5850429.sra 2020-06-21T10:29:22 prefetch.2.10.7: 1) Downloading 'SRR5850430'... 2020-06-21T10:29:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:14 prefetch.2.10.7: 'SRR5850430' is valid 2020-06-21T10:30:14 prefetch.2.10.7: 1) 'SRR5850430' was downloaded successfully 2020-06-21T10:30:14 prefetch.2.10.7: 'SRR5850430' has 0 unresolved dependencies Read 6742952 spots for SRR5850430/SRR5850430.sra Written 6742952 spots for SRR5850430/SRR5850430.sra 2020-06-21T10:30:46 prefetch.2.10.7: 1) Downloading 'SRR5850431'... 2020-06-21T10:30:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:57 prefetch.2.10.7: 'SRR5850431' is valid 2020-06-21T10:31:57 prefetch.2.10.7: 1) 'SRR5850431' was downloaded successfully 2020-06-21T10:31:57 prefetch.2.10.7: 'SRR5850431' has 0 unresolved dependencies Read 6680186 spots for SRR5850431/SRR5850431.sra Written 6680186 spots for SRR5850431/SRR5850431.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: 00:00:01 Multiseed full-index search: 00:06:16 26896532 reads; of these: 26896532 (100.00%) were unpaired; of these: 6670402 (24.80%) aligned 0 times 15244453 (56.68%) aligned exactly 1 time 4981677 (18.52%) aligned >1 times 75.20% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 3211799 / 20226130 = 0.1588 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 19:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.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 19:43:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:24: 1000000 INFO @ Sun, 21 Jun 2020 19:43:30: 2000000 INFO @ Sun, 21 Jun 2020 19:43:36: 3000000 INFO @ Sun, 21 Jun 2020 19:43:42: 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 19:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.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 19:43:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:49: 5000000 INFO @ Sun, 21 Jun 2020 19:43:54: 1000000 INFO @ Sun, 21 Jun 2020 19:43:55: 6000000 INFO @ Sun, 21 Jun 2020 19:44:01: 2000000 INFO @ Sun, 21 Jun 2020 19:44:02: 7000000 INFO @ Sun, 21 Jun 2020 19:44:07: 3000000 INFO @ Sun, 21 Jun 2020 19:44:08: 8000000 INFO @ Sun, 21 Jun 2020 19:44:14: 4000000 INFO @ Sun, 21 Jun 2020 19:44:15: 9000000 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 19:44:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.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 19:44:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:21: 5000000 INFO @ Sun, 21 Jun 2020 19:44:21: 10000000 INFO @ Sun, 21 Jun 2020 19:44:25: 1000000 INFO @ Sun, 21 Jun 2020 19:44:27: 6000000 INFO @ Sun, 21 Jun 2020 19:44:28: 11000000 INFO @ Sun, 21 Jun 2020 19:44:32: 2000000 INFO @ Sun, 21 Jun 2020 19:44:34: 7000000 INFO @ Sun, 21 Jun 2020 19:44:35: 12000000 INFO @ Sun, 21 Jun 2020 19:44:38: 3000000 INFO @ Sun, 21 Jun 2020 19:44:41: 13000000 INFO @ Sun, 21 Jun 2020 19:44:41: 8000000 INFO @ Sun, 21 Jun 2020 19:44:45: 4000000 INFO @ Sun, 21 Jun 2020 19:44:48: 14000000 INFO @ Sun, 21 Jun 2020 19:44:48: 9000000 INFO @ Sun, 21 Jun 2020 19:44:52: 5000000 INFO @ Sun, 21 Jun 2020 19:44:55: 15000000 INFO @ Sun, 21 Jun 2020 19:44:55: 10000000 INFO @ Sun, 21 Jun 2020 19:44:59: 6000000 INFO @ Sun, 21 Jun 2020 19:45:01: 16000000 INFO @ Sun, 21 Jun 2020 19:45:01: 11000000 INFO @ Sun, 21 Jun 2020 19:45:06: 7000000 INFO @ Sun, 21 Jun 2020 19:45:08: 17000000 INFO @ Sun, 21 Jun 2020 19:45:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:08: #1 total tags in treatment: 17014331 INFO @ Sun, 21 Jun 2020 19:45:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:08: #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 19:45:08: 12000000 INFO @ Sun, 21 Jun 2020 19:45:08: #1 tags after filtering in treatment: 17014228 INFO @ Sun, 21 Jun 2020 19:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:10: #2 number of paired peaks: 1016 INFO @ Sun, 21 Jun 2020 19:45:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:10: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:45:10: #2 alternative fragment length(s) may be 2,63 bps INFO @ Sun, 21 Jun 2020 19:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.05_model.r WARNING @ Sun, 21 Jun 2020 19:45:10: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:45:10: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Sun, 21 Jun 2020 19:45:10: #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 19:45:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:12: 8000000 INFO @ Sun, 21 Jun 2020 19:45:14: 13000000 INFO @ Sun, 21 Jun 2020 19:45:19: 9000000 INFO @ Sun, 21 Jun 2020 19:45:21: 14000000 INFO @ Sun, 21 Jun 2020 19:45:25: 10000000 INFO @ Sun, 21 Jun 2020 19:45:28: 15000000 INFO @ Sun, 21 Jun 2020 19:45:31: 11000000 INFO @ Sun, 21 Jun 2020 19:45:34: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:45:37: 12000000 INFO @ Sun, 21 Jun 2020 19:45:41: 17000000 INFO @ Sun, 21 Jun 2020 19:45:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:41: #1 total tags in treatment: 17014331 INFO @ Sun, 21 Jun 2020 19:45:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:41: #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 19:45:42: #1 tags after filtering in treatment: 17014228 INFO @ Sun, 21 Jun 2020 19:45:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:43: #2 number of paired peaks: 1016 INFO @ Sun, 21 Jun 2020 19:45:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:43: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:45:43: #2 alternative fragment length(s) may be 2,63 bps INFO @ Sun, 21 Jun 2020 19:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.10_model.r WARNING @ Sun, 21 Jun 2020 19:45:43: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:45:43: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Sun, 21 Jun 2020 19:45:43: #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 19:45:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:43: 13000000 INFO @ Sun, 21 Jun 2020 19:45:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:49: 14000000 INFO @ Sun, 21 Jun 2020 19:45:56: 15000000 INFO @ Sun, 21 Jun 2020 19:46:02: 16000000 INFO @ Sun, 21 Jun 2020 19:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.05_summits.bed INFO @ Sun, 21 Jun 2020 19:46:03: Done! pass1 - making usageList (467 chroms): 1 millis pass2 - checking and writing primary data (2826 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:46:08: 17000000 INFO @ Sun, 21 Jun 2020 19:46:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:08: #1 total tags in treatment: 17014331 INFO @ Sun, 21 Jun 2020 19:46:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:08: #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 19:46:08: #1 tags after filtering in treatment: 17014228 INFO @ Sun, 21 Jun 2020 19:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:10: #2 number of paired peaks: 1016 INFO @ Sun, 21 Jun 2020 19:46:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:10: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:46:10: #2 alternative fragment length(s) may be 2,63 bps INFO @ Sun, 21 Jun 2020 19:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.20_model.r WARNING @ Sun, 21 Jun 2020 19:46:10: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:46:10: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Sun, 21 Jun 2020 19:46:10: #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 19:46:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:46:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.10_summits.bed INFO @ Sun, 21 Jun 2020 19:46:39: Done! pass1 - making usageList (301 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:46:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020542/SRX3020542.20_summits.bed INFO @ Sun, 21 Jun 2020 19:47:05: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 6 millis CompletedMACS2peakCalling