Job ID = 6527403 SRX = SRX2350726 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:08:04 prefetch.2.10.7: 1) Downloading 'SRR5024035'... 2020-06-29T12:08:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:11:09 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:11:09 prefetch.2.10.7: 1) 'SRR5024035' was downloaded successfully Read 15764843 spots for SRR5024035/SRR5024035.sra Written 15764843 spots for SRR5024035/SRR5024035.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: 00:03:19 15764843 reads; of these: 15764843 (100.00%) were unpaired; of these: 222173 (1.41%) aligned 0 times 12763486 (80.96%) aligned exactly 1 time 2779184 (17.63%) aligned >1 times 98.59% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1722498 / 15542670 = 0.1108 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 @ Mon, 29 Jun 2020 21:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.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 @ Mon, 29 Jun 2020 21:25:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:25:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:25:22: 1000000 INFO @ Mon, 29 Jun 2020 21:25:26: 2000000 INFO @ Mon, 29 Jun 2020 21:25:31: 3000000 INFO @ Mon, 29 Jun 2020 21:25:36: 4000000 INFO @ Mon, 29 Jun 2020 21:25:41: 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 @ Mon, 29 Jun 2020 21:25:45: 6000000 INFO @ Mon, 29 Jun 2020 21:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.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 @ Mon, 29 Jun 2020 21:25:47: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:25:47: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:25:50: 7000000 INFO @ Mon, 29 Jun 2020 21:25:52: 1000000 INFO @ Mon, 29 Jun 2020 21:25:56: 8000000 INFO @ Mon, 29 Jun 2020 21:25:57: 2000000 INFO @ Mon, 29 Jun 2020 21:26:01: 9000000 INFO @ Mon, 29 Jun 2020 21:26:02: 3000000 INFO @ Mon, 29 Jun 2020 21:26:06: 10000000 INFO @ Mon, 29 Jun 2020 21:26:07: 4000000 INFO @ Mon, 29 Jun 2020 21:26:11: 11000000 INFO @ Mon, 29 Jun 2020 21:26:12: 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 @ Mon, 29 Jun 2020 21:26:16: 12000000 INFO @ Mon, 29 Jun 2020 21:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.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 @ Mon, 29 Jun 2020 21:26:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:26:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:26:17: 6000000 INFO @ Mon, 29 Jun 2020 21:26:21: 13000000 INFO @ Mon, 29 Jun 2020 21:26:22: 1000000 INFO @ Mon, 29 Jun 2020 21:26:22: 7000000 INFO @ Mon, 29 Jun 2020 21:26:25: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:26:25: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:26:25: #1 total tags in treatment: 13820172 INFO @ Mon, 29 Jun 2020 21:26:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:26:25: #1 tags after filtering in treatment: 13820172 INFO @ Mon, 29 Jun 2020 21:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:26:25: #1 finished! INFO @ Mon, 29 Jun 2020 21:26:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:26:26: #2 number of paired peaks: 285 WARNING @ Mon, 29 Jun 2020 21:26:26: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Mon, 29 Jun 2020 21:26:26: start model_add_line... INFO @ Mon, 29 Jun 2020 21:26:26: start X-correlation... INFO @ Mon, 29 Jun 2020 21:26:26: end of X-cor INFO @ Mon, 29 Jun 2020 21:26:26: #2 finished! INFO @ Mon, 29 Jun 2020 21:26:26: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 21:26:26: #2 alternative fragment length(s) may be 1,44,569,574 bps INFO @ Mon, 29 Jun 2020 21:26:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.05_model.r WARNING @ Mon, 29 Jun 2020 21:26:26: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:26:26: #2 You may need to consider one of the other alternative d(s): 1,44,569,574 WARNING @ Mon, 29 Jun 2020 21:26:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:26:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:26:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:26:27: 2000000 INFO @ Mon, 29 Jun 2020 21:26:27: 8000000 INFO @ Mon, 29 Jun 2020 21:26:32: 9000000 INFO @ Mon, 29 Jun 2020 21:26:32: 3000000 INFO @ Mon, 29 Jun 2020 21:26:37: 10000000 INFO @ Mon, 29 Jun 2020 21:26:37: 4000000 INFO @ Mon, 29 Jun 2020 21:26:42: 11000000 INFO @ Mon, 29 Jun 2020 21:26:42: 5000000 INFO @ Mon, 29 Jun 2020 21:26:46: 12000000 INFO @ Mon, 29 Jun 2020 21:26:47: 6000000 INFO @ Mon, 29 Jun 2020 21:26:49: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:26:51: 13000000 INFO @ Mon, 29 Jun 2020 21:26:52: 7000000 INFO @ Mon, 29 Jun 2020 21:26:55: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:26:55: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:26:55: #1 total tags in treatment: 13820172 INFO @ Mon, 29 Jun 2020 21:26:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:26:55: #1 tags after filtering in treatment: 13820172 INFO @ Mon, 29 Jun 2020 21:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:26:55: #1 finished! INFO @ Mon, 29 Jun 2020 21:26:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:26:56: #2 number of paired peaks: 285 WARNING @ Mon, 29 Jun 2020 21:26:56: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Mon, 29 Jun 2020 21:26:56: start model_add_line... INFO @ Mon, 29 Jun 2020 21:26:57: start X-correlation... INFO @ Mon, 29 Jun 2020 21:26:57: end of X-cor INFO @ Mon, 29 Jun 2020 21:26:57: #2 finished! INFO @ Mon, 29 Jun 2020 21:26:57: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 21:26:57: #2 alternative fragment length(s) may be 1,44,569,574 bps INFO @ Mon, 29 Jun 2020 21:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.10_model.r WARNING @ Mon, 29 Jun 2020 21:26:57: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:26:57: #2 You may need to consider one of the other alternative d(s): 1,44,569,574 WARNING @ Mon, 29 Jun 2020 21:26:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:26:57: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:26:57: 8000000 INFO @ Mon, 29 Jun 2020 21:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.05_summits.bed INFO @ Mon, 29 Jun 2020 21:27:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:27:02: 9000000 INFO @ Mon, 29 Jun 2020 21:27:07: 10000000 INFO @ Mon, 29 Jun 2020 21:27:12: 11000000 INFO @ Mon, 29 Jun 2020 21:27:17: 12000000 INFO @ Mon, 29 Jun 2020 21:27:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:27:22: 13000000 INFO @ Mon, 29 Jun 2020 21:27:27: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:27:27: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:27:27: #1 total tags in treatment: 13820172 INFO @ Mon, 29 Jun 2020 21:27:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:27:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:27:27: #1 tags after filtering in treatment: 13820172 INFO @ Mon, 29 Jun 2020 21:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:27:27: #1 finished! INFO @ Mon, 29 Jun 2020 21:27:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:27:28: #2 number of paired peaks: 285 WARNING @ Mon, 29 Jun 2020 21:27:28: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Mon, 29 Jun 2020 21:27:28: start model_add_line... INFO @ Mon, 29 Jun 2020 21:27:28: start X-correlation... INFO @ Mon, 29 Jun 2020 21:27:28: end of X-cor INFO @ Mon, 29 Jun 2020 21:27:28: #2 finished! INFO @ Mon, 29 Jun 2020 21:27:28: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 21:27:28: #2 alternative fragment length(s) may be 1,44,569,574 bps INFO @ Mon, 29 Jun 2020 21:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.20_model.r WARNING @ Mon, 29 Jun 2020 21:27:28: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:27:28: #2 You may need to consider one of the other alternative d(s): 1,44,569,574 WARNING @ Mon, 29 Jun 2020 21:27:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:27:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.10_summits.bed INFO @ Mon, 29 Jun 2020 21:27:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:27:51: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350726/SRX2350726.20_summits.bed INFO @ Mon, 29 Jun 2020 21:28:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。