Job ID = 6455869 SRX = SRX3020535 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:22:35 prefetch.2.10.7: 1) Downloading 'SRR5850400'... 2020-06-21T10:22:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:39 prefetch.2.10.7: 'SRR5850400' is valid 2020-06-21T10:23:39 prefetch.2.10.7: 1) 'SRR5850400' was downloaded successfully 2020-06-21T10:23:39 prefetch.2.10.7: 'SRR5850400' has 0 unresolved dependencies Read 5678184 spots for SRR5850400/SRR5850400.sra Written 5678184 spots for SRR5850400/SRR5850400.sra 2020-06-21T10:24:08 prefetch.2.10.7: 1) Downloading 'SRR5850401'... 2020-06-21T10:24:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:46 prefetch.2.10.7: 'SRR5850401' is valid 2020-06-21T10:24:46 prefetch.2.10.7: 1) 'SRR5850401' was downloaded successfully 2020-06-21T10:24:46 prefetch.2.10.7: 'SRR5850401' has 0 unresolved dependencies Read 5614258 spots for SRR5850401/SRR5850401.sra Written 5614258 spots for SRR5850401/SRR5850401.sra 2020-06-21T10:25:14 prefetch.2.10.7: 1) Downloading 'SRR5850402'... 2020-06-21T10:25:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:51 prefetch.2.10.7: 'SRR5850402' is valid 2020-06-21T10:25:51 prefetch.2.10.7: 1) 'SRR5850402' was downloaded successfully 2020-06-21T10:25:51 prefetch.2.10.7: 'SRR5850402' has 0 unresolved dependencies Read 5604279 spots for SRR5850402/SRR5850402.sra Written 5604279 spots for SRR5850402/SRR5850402.sra 2020-06-21T10:26:19 prefetch.2.10.7: 1) Downloading 'SRR5850403'... 2020-06-21T10:26:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:03 prefetch.2.10.7: 'SRR5850403' is valid 2020-06-21T10:27:03 prefetch.2.10.7: 1) 'SRR5850403' was downloaded successfully 2020-06-21T10:27:03 prefetch.2.10.7: 'SRR5850403' has 0 unresolved dependencies Read 5562042 spots for SRR5850403/SRR5850403.sra Written 5562042 spots for SRR5850403/SRR5850403.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 22458763 reads; of these: 22458763 (100.00%) were unpaired; of these: 798190 (3.55%) aligned 0 times 15910391 (70.84%) aligned exactly 1 time 5750182 (25.60%) aligned >1 times 96.45% 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] 3969884 / 21660573 = 0.1833 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 19:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.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 19:38:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:27: 1000000 INFO @ Sun, 21 Jun 2020 19:38:32: 2000000 INFO @ Sun, 21 Jun 2020 19:38:37: 3000000 INFO @ Sun, 21 Jun 2020 19:38:42: 4000000 INFO @ Sun, 21 Jun 2020 19:38:47: 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 19:38:52: 6000000 INFO @ Sun, 21 Jun 2020 19:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.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 19:38:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:56: 7000000 INFO @ Sun, 21 Jun 2020 19:38:57: 1000000 INFO @ Sun, 21 Jun 2020 19:39:01: 8000000 INFO @ Sun, 21 Jun 2020 19:39:02: 2000000 INFO @ Sun, 21 Jun 2020 19:39:06: 9000000 INFO @ Sun, 21 Jun 2020 19:39:07: 3000000 INFO @ Sun, 21 Jun 2020 19:39:11: 10000000 INFO @ Sun, 21 Jun 2020 19:39:12: 4000000 INFO @ Sun, 21 Jun 2020 19:39:16: 11000000 INFO @ Sun, 21 Jun 2020 19:39:17: 5000000 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 19:39:21: 12000000 INFO @ Sun, 21 Jun 2020 19:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.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 19:39:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:22: 6000000 INFO @ Sun, 21 Jun 2020 19:39:26: 13000000 INFO @ Sun, 21 Jun 2020 19:39:27: 7000000 INFO @ Sun, 21 Jun 2020 19:39:27: 1000000 INFO @ Sun, 21 Jun 2020 19:39:30: 14000000 INFO @ Sun, 21 Jun 2020 19:39:32: 8000000 INFO @ Sun, 21 Jun 2020 19:39:32: 2000000 INFO @ Sun, 21 Jun 2020 19:39:36: 15000000 INFO @ Sun, 21 Jun 2020 19:39:37: 9000000 INFO @ Sun, 21 Jun 2020 19:39:37: 3000000 INFO @ Sun, 21 Jun 2020 19:39:41: 16000000 INFO @ Sun, 21 Jun 2020 19:39:41: 10000000 INFO @ Sun, 21 Jun 2020 19:39:42: 4000000 INFO @ Sun, 21 Jun 2020 19:39:46: 17000000 INFO @ Sun, 21 Jun 2020 19:39:46: 11000000 INFO @ Sun, 21 Jun 2020 19:39:47: 5000000 INFO @ Sun, 21 Jun 2020 19:39:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:39:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:39:50: #1 total tags in treatment: 17690689 INFO @ Sun, 21 Jun 2020 19:39:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:50: #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 19:39:50: #1 tags after filtering in treatment: 17690615 INFO @ Sun, 21 Jun 2020 19:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:51: 12000000 INFO @ Sun, 21 Jun 2020 19:39:51: #2 number of paired peaks: 1967 INFO @ Sun, 21 Jun 2020 19:39:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:52: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 19:39:52: #2 alternative fragment length(s) may be 2,90 bps INFO @ Sun, 21 Jun 2020 19:39:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.05_model.r WARNING @ Sun, 21 Jun 2020 19:39:52: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:52: #2 You may need to consider one of the other alternative d(s): 2,90 WARNING @ Sun, 21 Jun 2020 19:39:52: #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 19:39:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:52: 6000000 INFO @ Sun, 21 Jun 2020 19:39:56: 13000000 INFO @ Sun, 21 Jun 2020 19:39:57: 7000000 INFO @ Sun, 21 Jun 2020 19:40:01: 14000000 INFO @ Sun, 21 Jun 2020 19:40:02: 8000000 INFO @ Sun, 21 Jun 2020 19:40:06: 15000000 INFO @ Sun, 21 Jun 2020 19:40:06: 9000000 INFO @ Sun, 21 Jun 2020 19:40:11: 16000000 INFO @ Sun, 21 Jun 2020 19:40:11: 10000000 INFO @ Sun, 21 Jun 2020 19:40:16: 17000000 INFO @ Sun, 21 Jun 2020 19:40:16: 11000000 INFO @ Sun, 21 Jun 2020 19:40:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:20: #1 total tags in treatment: 17690689 INFO @ Sun, 21 Jun 2020 19:40:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:20: #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 19:40:20: #1 tags after filtering in treatment: 17690615 INFO @ Sun, 21 Jun 2020 19:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:21: 12000000 INFO @ Sun, 21 Jun 2020 19:40:21: #2 number of paired peaks: 1967 INFO @ Sun, 21 Jun 2020 19:40:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:22: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 19:40:22: #2 alternative fragment length(s) may be 2,90 bps INFO @ Sun, 21 Jun 2020 19:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.10_model.r WARNING @ Sun, 21 Jun 2020 19:40:22: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:22: #2 You may need to consider one of the other alternative d(s): 2,90 WARNING @ Sun, 21 Jun 2020 19:40:22: #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 19:40:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:26: 13000000 INFO @ Sun, 21 Jun 2020 19:40:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:30: 14000000 INFO @ Sun, 21 Jun 2020 19:40:36: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:40:40: 16000000 INFO @ Sun, 21 Jun 2020 19:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.05_summits.bed INFO @ Sun, 21 Jun 2020 19:40:45: Done! pass1 - making usageList (567 chroms): 2 millis pass2 - checking and writing primary data (6885 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:40:45: 17000000 INFO @ Sun, 21 Jun 2020 19:40:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:49: #1 total tags in treatment: 17690689 INFO @ Sun, 21 Jun 2020 19:40:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:49: #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 19:40:50: #1 tags after filtering in treatment: 17690615 INFO @ Sun, 21 Jun 2020 19:40:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:51: #2 number of paired peaks: 1967 INFO @ Sun, 21 Jun 2020 19:40:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:51: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 19:40:51: #2 alternative fragment length(s) may be 2,90 bps INFO @ Sun, 21 Jun 2020 19:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.20_model.r WARNING @ Sun, 21 Jun 2020 19:40:51: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:51: #2 You may need to consider one of the other alternative d(s): 2,90 WARNING @ Sun, 21 Jun 2020 19:40:51: #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 19:40:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:17: Done! pass1 - making usageList (450 chroms): 2 millis pass2 - checking and writing primary data (2737 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020535/SRX3020535.20_summits.bed INFO @ Sun, 21 Jun 2020 19:41:46: Done! pass1 - making usageList (267 chroms): 2 millis pass2 - checking and writing primary data (803 records, 4 fields): 10 millis CompletedMACS2peakCalling