Job ID = 6367904 SRX = SRX4194197 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:48:36 prefetch.2.10.7: 1) Downloading 'SRR7291475'... 2020-06-15T23:48:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:55 prefetch.2.10.7: 'SRR7291475' is valid 2020-06-15T23:49:55 prefetch.2.10.7: 1) 'SRR7291475' was downloaded successfully 2020-06-15T23:49:55 prefetch.2.10.7: 'SRR7291475' has 0 unresolved dependencies Read 5903405 spots for SRR7291475/SRR7291475.sra Written 5903405 spots for SRR7291475/SRR7291475.sra 2020-06-15T23:50:31 prefetch.2.10.7: 1) Downloading 'SRR7291476'... 2020-06-15T23:50:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:25 prefetch.2.10.7: 'SRR7291476' is valid 2020-06-15T23:51:25 prefetch.2.10.7: 1) 'SRR7291476' was downloaded successfully 2020-06-15T23:51:25 prefetch.2.10.7: 'SRR7291476' has 0 unresolved dependencies Read 5778026 spots for SRR7291476/SRR7291476.sra Written 5778026 spots for SRR7291476/SRR7291476.sra 2020-06-15T23:51:59 prefetch.2.10.7: 1) Downloading 'SRR7291477'... 2020-06-15T23:51:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:04 prefetch.2.10.7: 'SRR7291477' is valid 2020-06-15T23:53:04 prefetch.2.10.7: 1) 'SRR7291477' was downloaded successfully 2020-06-15T23:53:04 prefetch.2.10.7: 'SRR7291477' has 0 unresolved dependencies Read 5900969 spots for SRR7291477/SRR7291477.sra Written 5900969 spots for SRR7291477/SRR7291477.sra 2020-06-15T23:53:39 prefetch.2.10.7: 1) Downloading 'SRR7291478'... 2020-06-15T23:53:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:23 prefetch.2.10.7: 'SRR7291478' is valid 2020-06-15T23:54:23 prefetch.2.10.7: 1) 'SRR7291478' was downloaded successfully 2020-06-15T23:54:23 prefetch.2.10.7: 'SRR7291478' has 0 unresolved dependencies Read 5720230 spots for SRR7291478/SRR7291478.sra Written 5720230 spots for SRR7291478/SRR7291478.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: 00:09:26 23302630 reads; of these: 23302630 (100.00%) were unpaired; of these: 497490 (2.13%) aligned 0 times 18368169 (78.82%) aligned exactly 1 time 4436971 (19.04%) aligned >1 times 97.87% overall alignment rate Time searching: 00:09:26 Overall time: 00:09:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8094721 / 22805140 = 0.3550 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 @ Tue, 16 Jun 2020 09:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:11:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:21: 1000000 INFO @ Tue, 16 Jun 2020 09:11:28: 2000000 INFO @ Tue, 16 Jun 2020 09:11:34: 3000000 INFO @ Tue, 16 Jun 2020 09:11:40: 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 @ Tue, 16 Jun 2020 09:11:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:11:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:47: 5000000 INFO @ Tue, 16 Jun 2020 09:11:52: 1000000 INFO @ Tue, 16 Jun 2020 09:11:54: 6000000 INFO @ Tue, 16 Jun 2020 09:11:59: 2000000 INFO @ Tue, 16 Jun 2020 09:12:00: 7000000 INFO @ Tue, 16 Jun 2020 09:12:06: 3000000 INFO @ Tue, 16 Jun 2020 09:12:08: 8000000 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 @ Tue, 16 Jun 2020 09:12:13: 4000000 INFO @ Tue, 16 Jun 2020 09:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:12:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:15: 9000000 INFO @ Tue, 16 Jun 2020 09:12:20: 5000000 INFO @ Tue, 16 Jun 2020 09:12:22: 10000000 INFO @ Tue, 16 Jun 2020 09:12:22: 1000000 INFO @ Tue, 16 Jun 2020 09:12:27: 6000000 INFO @ Tue, 16 Jun 2020 09:12:28: 11000000 INFO @ Tue, 16 Jun 2020 09:12:29: 2000000 INFO @ Tue, 16 Jun 2020 09:12:34: 7000000 INFO @ Tue, 16 Jun 2020 09:12:35: 12000000 INFO @ Tue, 16 Jun 2020 09:12:36: 3000000 INFO @ Tue, 16 Jun 2020 09:12:41: 8000000 INFO @ Tue, 16 Jun 2020 09:12:42: 13000000 INFO @ Tue, 16 Jun 2020 09:12:43: 4000000 INFO @ Tue, 16 Jun 2020 09:12:48: 9000000 INFO @ Tue, 16 Jun 2020 09:12:49: 14000000 INFO @ Tue, 16 Jun 2020 09:12:50: 5000000 INFO @ Tue, 16 Jun 2020 09:12:54: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:12:54: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:12:54: #1 total tags in treatment: 14710419 INFO @ Tue, 16 Jun 2020 09:12:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:54: #1 tags after filtering in treatment: 14710419 INFO @ Tue, 16 Jun 2020 09:12:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:55: 10000000 INFO @ Tue, 16 Jun 2020 09:12:55: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 09:12:55: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:55: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:12:55: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:12:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:55: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:12:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:12:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:56: 6000000 INFO @ Tue, 16 Jun 2020 09:13:01: 11000000 INFO @ Tue, 16 Jun 2020 09:13:03: 7000000 INFO @ Tue, 16 Jun 2020 09:13:08: 12000000 INFO @ Tue, 16 Jun 2020 09:13:10: 8000000 INFO @ Tue, 16 Jun 2020 09:13:14: 13000000 INFO @ Tue, 16 Jun 2020 09:13:17: 9000000 INFO @ Tue, 16 Jun 2020 09:13:21: 14000000 INFO @ Tue, 16 Jun 2020 09:13:23: 10000000 INFO @ Tue, 16 Jun 2020 09:13:26: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:13:26: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:13:26: #1 total tags in treatment: 14710419 INFO @ Tue, 16 Jun 2020 09:13:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:13:26: #1 tags after filtering in treatment: 14710419 INFO @ Tue, 16 Jun 2020 09:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:27: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 09:13:27: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:27: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:13:27: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.10_model.r WARNING @ Tue, 16 Jun 2020 09:13:27: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:27: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:13:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:13:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:29: 11000000 INFO @ Tue, 16 Jun 2020 09:13:36: 12000000 INFO @ Tue, 16 Jun 2020 09:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:42: 13000000 INFO @ Tue, 16 Jun 2020 09:13:48: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:52: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:13:52: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:13:52: #1 total tags in treatment: 14710419 INFO @ Tue, 16 Jun 2020 09:13:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:13:52: #1 tags after filtering in treatment: 14710419 INFO @ Tue, 16 Jun 2020 09:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:53: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 09:13:53: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:54: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:13:54: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:13:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:54: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:54: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:13:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:13:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194197/SRX4194197.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling