Job ID = 6455873 SRX = SRX3020539 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:21:06 prefetch.2.10.7: 1) Downloading 'SRR5850416'... 2020-06-21T10:21:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:45 prefetch.2.10.7: 'SRR5850416' is valid 2020-06-21T10:21:45 prefetch.2.10.7: 1) 'SRR5850416' was downloaded successfully 2020-06-21T10:21:45 prefetch.2.10.7: 'SRR5850416' has 0 unresolved dependencies Read 5135703 spots for SRR5850416/SRR5850416.sra Written 5135703 spots for SRR5850416/SRR5850416.sra 2020-06-21T10:22:13 prefetch.2.10.7: 1) Downloading 'SRR5850417'... 2020-06-21T10:22:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:52 prefetch.2.10.7: 'SRR5850417' is valid 2020-06-21T10:22:52 prefetch.2.10.7: 1) 'SRR5850417' was downloaded successfully 2020-06-21T10:22:52 prefetch.2.10.7: 'SRR5850417' has 0 unresolved dependencies Read 5064659 spots for SRR5850417/SRR5850417.sra Written 5064659 spots for SRR5850417/SRR5850417.sra 2020-06-21T10:23:19 prefetch.2.10.7: 1) Downloading 'SRR5850418'... 2020-06-21T10:23:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:06 prefetch.2.10.7: 'SRR5850418' is valid 2020-06-21T10:24:06 prefetch.2.10.7: 1) 'SRR5850418' was downloaded successfully 2020-06-21T10:24:06 prefetch.2.10.7: 'SRR5850418' has 0 unresolved dependencies Read 5077820 spots for SRR5850418/SRR5850418.sra Written 5077820 spots for SRR5850418/SRR5850418.sra 2020-06-21T10:24:33 prefetch.2.10.7: 1) Downloading 'SRR5850419'... 2020-06-21T10:24:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:18 prefetch.2.10.7: 'SRR5850419' is valid 2020-06-21T10:25:18 prefetch.2.10.7: 1) 'SRR5850419' was downloaded successfully 2020-06-21T10:25:18 prefetch.2.10.7: 'SRR5850419' has 0 unresolved dependencies Read 5032197 spots for SRR5850419/SRR5850419.sra Written 5032197 spots for SRR5850419/SRR5850419.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: 00:05:20 20310379 reads; of these: 20310379 (100.00%) were unpaired; of these: 630865 (3.11%) aligned 0 times 15043859 (74.07%) aligned exactly 1 time 4635655 (22.82%) aligned >1 times 96.89% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 3124827 / 19679514 = 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 19:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.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 19:35:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:27: 1000000 INFO @ Sun, 21 Jun 2020 19:35:32: 2000000 INFO @ Sun, 21 Jun 2020 19:35:37: 3000000 INFO @ Sun, 21 Jun 2020 19:35:43: 4000000 INFO @ Sun, 21 Jun 2020 19:35:48: 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 19:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.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 19:35:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:53: 6000000 INFO @ Sun, 21 Jun 2020 19:35:56: 1000000 INFO @ Sun, 21 Jun 2020 19:35:59: 7000000 INFO @ Sun, 21 Jun 2020 19:36:01: 2000000 INFO @ Sun, 21 Jun 2020 19:36:04: 8000000 INFO @ Sun, 21 Jun 2020 19:36:06: 3000000 INFO @ Sun, 21 Jun 2020 19:36:10: 9000000 INFO @ Sun, 21 Jun 2020 19:36:12: 4000000 INFO @ Sun, 21 Jun 2020 19:36:15: 10000000 INFO @ Sun, 21 Jun 2020 19:36:17: 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 19:36:20: 11000000 INFO @ Sun, 21 Jun 2020 19:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.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 19:36:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:23: 6000000 INFO @ Sun, 21 Jun 2020 19:36:27: 12000000 INFO @ Sun, 21 Jun 2020 19:36:28: 1000000 INFO @ Sun, 21 Jun 2020 19:36:29: 7000000 INFO @ Sun, 21 Jun 2020 19:36:33: 13000000 INFO @ Sun, 21 Jun 2020 19:36:35: 2000000 INFO @ Sun, 21 Jun 2020 19:36:36: 8000000 INFO @ Sun, 21 Jun 2020 19:36:40: 14000000 INFO @ Sun, 21 Jun 2020 19:36:42: 3000000 INFO @ Sun, 21 Jun 2020 19:36:42: 9000000 INFO @ Sun, 21 Jun 2020 19:36:46: 15000000 INFO @ Sun, 21 Jun 2020 19:36:49: 10000000 INFO @ Sun, 21 Jun 2020 19:36:49: 4000000 INFO @ Sun, 21 Jun 2020 19:36:53: 16000000 INFO @ Sun, 21 Jun 2020 19:36:55: 11000000 INFO @ Sun, 21 Jun 2020 19:36:56: 5000000 INFO @ Sun, 21 Jun 2020 19:36:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:57: #1 total tags in treatment: 16554687 INFO @ Sun, 21 Jun 2020 19:36:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:57: #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 19:36:57: #1 tags after filtering in treatment: 16554589 INFO @ Sun, 21 Jun 2020 19:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:58: #2 number of paired peaks: 1391 INFO @ Sun, 21 Jun 2020 19:36:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:58: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 19:36:58: #2 alternative fragment length(s) may be 2,91 bps INFO @ Sun, 21 Jun 2020 19:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.05_model.r WARNING @ Sun, 21 Jun 2020 19:36:58: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:58: #2 You may need to consider one of the other alternative d(s): 2,91 WARNING @ Sun, 21 Jun 2020 19:36:58: #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 19:36:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:01: 12000000 INFO @ Sun, 21 Jun 2020 19:37:03: 6000000 INFO @ Sun, 21 Jun 2020 19:37:08: 13000000 INFO @ Sun, 21 Jun 2020 19:37:10: 7000000 INFO @ Sun, 21 Jun 2020 19:37:15: 14000000 INFO @ Sun, 21 Jun 2020 19:37:17: 8000000 INFO @ Sun, 21 Jun 2020 19:37:21: 15000000 INFO @ Sun, 21 Jun 2020 19:37:24: 9000000 INFO @ Sun, 21 Jun 2020 19:37:27: 16000000 INFO @ Sun, 21 Jun 2020 19:37:31: 10000000 INFO @ Sun, 21 Jun 2020 19:37:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:37:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:37:31: #1 total tags in treatment: 16554687 INFO @ Sun, 21 Jun 2020 19:37:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:31: #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 19:37:32: #1 tags after filtering in treatment: 16554589 INFO @ Sun, 21 Jun 2020 19:37:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:32: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:37:33: #2 number of paired peaks: 1391 INFO @ Sun, 21 Jun 2020 19:37:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:33: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 19:37:33: #2 alternative fragment length(s) may be 2,91 bps INFO @ Sun, 21 Jun 2020 19:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.10_model.r WARNING @ Sun, 21 Jun 2020 19:37:33: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:37:33: #2 You may need to consider one of the other alternative d(s): 2,91 WARNING @ Sun, 21 Jun 2020 19:37:33: #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 19:37:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:38: 11000000 INFO @ Sun, 21 Jun 2020 19:37:44: 12000000 INFO @ Sun, 21 Jun 2020 19:37:51: 13000000 INFO @ Sun, 21 Jun 2020 19:37:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.05_summits.bed INFO @ Sun, 21 Jun 2020 19:37:52: Done! pass1 - making usageList (438 chroms): 1 millis pass2 - checking and writing primary data (4452 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:58: 14000000 INFO @ Sun, 21 Jun 2020 19:38:04: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:38:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:10: 16000000 INFO @ Sun, 21 Jun 2020 19:38:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:38:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:38:14: #1 total tags in treatment: 16554687 INFO @ Sun, 21 Jun 2020 19:38:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:14: #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 19:38:15: #1 tags after filtering in treatment: 16554589 INFO @ Sun, 21 Jun 2020 19:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:16: #2 number of paired peaks: 1391 INFO @ Sun, 21 Jun 2020 19:38:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:16: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 19:38:16: #2 alternative fragment length(s) may be 2,91 bps INFO @ Sun, 21 Jun 2020 19:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.20_model.r WARNING @ Sun, 21 Jun 2020 19:38:16: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:16: #2 You may need to consider one of the other alternative d(s): 2,91 WARNING @ Sun, 21 Jun 2020 19:38:16: #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 19:38:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:27: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020539/SRX3020539.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:11: Done! pass1 - making usageList (150 chroms): 0 millis pass2 - checking and writing primary data (406 records, 4 fields): 6 millis CompletedMACS2peakCalling