Job ID = 6367009 SRX = SRX257707 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:53 prefetch.2.10.7: 1) Downloading 'SRR800726'... 2020-06-15T23:06:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:53 prefetch.2.10.7: 'SRR800726' is valid 2020-06-15T23:07:53 prefetch.2.10.7: 1) 'SRR800726' was downloaded successfully Read 7873433 spots for SRR800726/SRR800726.sra Written 7873433 spots for SRR800726/SRR800726.sra 2020-06-15T23:08:26 prefetch.2.10.7: 1) Downloading 'SRR800727'... 2020-06-15T23:08:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:45 prefetch.2.10.7: 'SRR800727' is valid 2020-06-15T23:09:45 prefetch.2.10.7: 1) 'SRR800727' was downloaded successfully Read 10198100 spots for SRR800727/SRR800727.sra Written 10198100 spots for SRR800727/SRR800727.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: 00:04:12 18071533 reads; of these: 18071533 (100.00%) were unpaired; of these: 379392 (2.10%) aligned 0 times 14716695 (81.44%) aligned exactly 1 time 2975446 (16.46%) aligned >1 times 97.90% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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 8 files... [bam_rmdupse_core] 1802671 / 17692141 = 0.1019 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 08:19:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.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 08:19:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:17: 1000000 INFO @ Tue, 16 Jun 2020 08:19:22: 2000000 INFO @ Tue, 16 Jun 2020 08:19:26: 3000000 INFO @ Tue, 16 Jun 2020 08:19:31: 4000000 INFO @ Tue, 16 Jun 2020 08:19:36: 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 @ Tue, 16 Jun 2020 08:19:41: 6000000 INFO @ Tue, 16 Jun 2020 08:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.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 08:19:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:46: 7000000 INFO @ Tue, 16 Jun 2020 08:19:47: 1000000 INFO @ Tue, 16 Jun 2020 08:19:51: 8000000 INFO @ Tue, 16 Jun 2020 08:19:53: 2000000 INFO @ Tue, 16 Jun 2020 08:19:56: 9000000 INFO @ Tue, 16 Jun 2020 08:19:59: 3000000 INFO @ Tue, 16 Jun 2020 08:20:01: 10000000 INFO @ Tue, 16 Jun 2020 08:20:04: 4000000 INFO @ Tue, 16 Jun 2020 08:20:06: 11000000 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 08:20:10: 5000000 INFO @ Tue, 16 Jun 2020 08:20:11: 12000000 INFO @ Tue, 16 Jun 2020 08:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.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 08:20:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:16: 13000000 INFO @ Tue, 16 Jun 2020 08:20:16: 6000000 INFO @ Tue, 16 Jun 2020 08:20:18: 1000000 INFO @ Tue, 16 Jun 2020 08:20:21: 14000000 INFO @ Tue, 16 Jun 2020 08:20:22: 7000000 INFO @ Tue, 16 Jun 2020 08:20:24: 2000000 INFO @ Tue, 16 Jun 2020 08:20:26: 15000000 INFO @ Tue, 16 Jun 2020 08:20:28: 8000000 INFO @ Tue, 16 Jun 2020 08:20:30: 3000000 INFO @ Tue, 16 Jun 2020 08:20:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:31: #1 total tags in treatment: 15889470 INFO @ Tue, 16 Jun 2020 08:20:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:31: #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 08:20:31: #1 tags after filtering in treatment: 15889470 INFO @ Tue, 16 Jun 2020 08:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:32: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 08:20:32: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:32: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:20:32: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 08:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:32: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 08:20:32: #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 08:20:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:34: 9000000 INFO @ Tue, 16 Jun 2020 08:20:35: 4000000 INFO @ Tue, 16 Jun 2020 08:20:39: 10000000 INFO @ Tue, 16 Jun 2020 08:20:41: 5000000 INFO @ Tue, 16 Jun 2020 08:20:45: 11000000 INFO @ Tue, 16 Jun 2020 08:20:47: 6000000 INFO @ Tue, 16 Jun 2020 08:20:51: 12000000 INFO @ Tue, 16 Jun 2020 08:20:52: 7000000 INFO @ Tue, 16 Jun 2020 08:20:56: 13000000 INFO @ Tue, 16 Jun 2020 08:20:58: 8000000 INFO @ Tue, 16 Jun 2020 08:20:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:02: 14000000 INFO @ Tue, 16 Jun 2020 08:21:04: 9000000 INFO @ Tue, 16 Jun 2020 08:21:08: 15000000 INFO @ Tue, 16 Jun 2020 08:21:09: 10000000 INFO @ Tue, 16 Jun 2020 08:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (711 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:13: #1 total tags in treatment: 15889470 INFO @ Tue, 16 Jun 2020 08:21:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:13: #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 08:21:13: #1 tags after filtering in treatment: 15889470 INFO @ Tue, 16 Jun 2020 08:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:14: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 08:21:14: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:14: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:21:14: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 08:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.10_model.r WARNING @ Tue, 16 Jun 2020 08:21:14: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:14: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 08:21:14: #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 08:21:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:15: 11000000 INFO @ Tue, 16 Jun 2020 08:21:20: 12000000 INFO @ Tue, 16 Jun 2020 08:21:26: 13000000 INFO @ Tue, 16 Jun 2020 08:21:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:37: 15000000 INFO @ Tue, 16 Jun 2020 08:21:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:42: #1 total tags in treatment: 15889470 INFO @ Tue, 16 Jun 2020 08:21:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:42: #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 08:21:42: #1 tags after filtering in treatment: 15889470 INFO @ Tue, 16 Jun 2020 08:21:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:44: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 08:21:44: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:44: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:21:44: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 08:21:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:44: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 08:21:44: #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 08:21:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257707/SRX257707.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling