Job ID = 6497532 SRX = SRX495122 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:10:11 prefetch.2.10.7: 1) Downloading 'SRR1198654'... 2020-06-25T22:10:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:12:52 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:12:52 prefetch.2.10.7: 1) 'SRR1198654' was downloaded successfully Read 22015477 spots for SRR1198654/SRR1198654.sra Written 22015477 spots for SRR1198654/SRR1198654.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: 00:05:04 22015477 reads; of these: 22015477 (100.00%) were unpaired; of these: 1904983 (8.65%) aligned 0 times 16767131 (76.16%) aligned exactly 1 time 3343363 (15.19%) aligned >1 times 91.35% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 5877832 / 20110494 = 0.2923 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 @ Fri, 26 Jun 2020 07:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.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 @ Fri, 26 Jun 2020 07:25:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:25:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:25:23: 1000000 INFO @ Fri, 26 Jun 2020 07:25:29: 2000000 INFO @ Fri, 26 Jun 2020 07:25:36: 3000000 INFO @ Fri, 26 Jun 2020 07:25:42: 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 @ Fri, 26 Jun 2020 07:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.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 @ Fri, 26 Jun 2020 07:25:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:25:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:25:49: 5000000 INFO @ Fri, 26 Jun 2020 07:25:52: 1000000 INFO @ Fri, 26 Jun 2020 07:25:56: 6000000 INFO @ Fri, 26 Jun 2020 07:25:58: 2000000 INFO @ Fri, 26 Jun 2020 07:26:03: 7000000 INFO @ Fri, 26 Jun 2020 07:26:04: 3000000 INFO @ Fri, 26 Jun 2020 07:26:09: 8000000 INFO @ Fri, 26 Jun 2020 07:26:10: 4000000 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 @ Fri, 26 Jun 2020 07:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.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 @ Fri, 26 Jun 2020 07:26:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:26:16: 9000000 INFO @ Fri, 26 Jun 2020 07:26:16: 5000000 INFO @ Fri, 26 Jun 2020 07:26:22: 6000000 INFO @ Fri, 26 Jun 2020 07:26:23: 10000000 INFO @ Fri, 26 Jun 2020 07:26:23: 1000000 INFO @ Fri, 26 Jun 2020 07:26:28: 7000000 INFO @ Fri, 26 Jun 2020 07:26:29: 11000000 INFO @ Fri, 26 Jun 2020 07:26:31: 2000000 INFO @ Fri, 26 Jun 2020 07:26:35: 8000000 INFO @ Fri, 26 Jun 2020 07:26:36: 12000000 INFO @ Fri, 26 Jun 2020 07:26:38: 3000000 INFO @ Fri, 26 Jun 2020 07:26:41: 9000000 INFO @ Fri, 26 Jun 2020 07:26:43: 13000000 INFO @ Fri, 26 Jun 2020 07:26:45: 4000000 INFO @ Fri, 26 Jun 2020 07:26:47: 10000000 INFO @ Fri, 26 Jun 2020 07:26:50: 14000000 INFO @ Fri, 26 Jun 2020 07:26:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:26:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:26:51: #1 total tags in treatment: 14232662 INFO @ Fri, 26 Jun 2020 07:26:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:26:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:26:52: #1 tags after filtering in treatment: 14232662 INFO @ Fri, 26 Jun 2020 07:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:26:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:26:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:26:53: 5000000 INFO @ Fri, 26 Jun 2020 07:26:53: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 07:26:53: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 07:26:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:26:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:26:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:26:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:26:53: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 07:26:53: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 07:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.05_model.r WARNING @ Fri, 26 Jun 2020 07:26:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:26:53: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 07:26:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:26:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:26:53: 11000000 INFO @ Fri, 26 Jun 2020 07:26:59: 6000000 INFO @ Fri, 26 Jun 2020 07:27:00: 12000000 INFO @ Fri, 26 Jun 2020 07:27:06: 13000000 INFO @ Fri, 26 Jun 2020 07:27:07: 7000000 INFO @ Fri, 26 Jun 2020 07:27:13: 14000000 INFO @ Fri, 26 Jun 2020 07:27:13: 8000000 INFO @ Fri, 26 Jun 2020 07:27:14: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:27:14: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:27:14: #1 total tags in treatment: 14232662 INFO @ Fri, 26 Jun 2020 07:27:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:27:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:27:15: #1 tags after filtering in treatment: 14232662 INFO @ Fri, 26 Jun 2020 07:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:27:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:27:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:27:16: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 07:27:16: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 07:27:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:27:16: start X-correlation... INFO @ Fri, 26 Jun 2020 07:27:16: end of X-cor INFO @ Fri, 26 Jun 2020 07:27:16: #2 finished! INFO @ Fri, 26 Jun 2020 07:27:16: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 07:27:16: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 07:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.10_model.r WARNING @ Fri, 26 Jun 2020 07:27:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:27:16: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 07:27:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:27:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:27:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:27:19: 9000000 INFO @ Fri, 26 Jun 2020 07:27:26: 10000000 INFO @ Fri, 26 Jun 2020 07:27:32: 11000000 INFO @ Fri, 26 Jun 2020 07:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.05_summits.bed INFO @ Fri, 26 Jun 2020 07:27:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:27:38: 12000000 INFO @ Fri, 26 Jun 2020 07:27:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:27:44: 13000000 INFO @ Fri, 26 Jun 2020 07:27:50: 14000000 INFO @ Fri, 26 Jun 2020 07:27:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:27:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:27:51: #1 total tags in treatment: 14232662 INFO @ Fri, 26 Jun 2020 07:27:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:27:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:27:52: #1 tags after filtering in treatment: 14232662 INFO @ Fri, 26 Jun 2020 07:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:27:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:27:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:27:53: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 07:27:53: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 07:27:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:27:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:27:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:27:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:27:53: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 07:27:53: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 07:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.20_model.r WARNING @ Fri, 26 Jun 2020 07:27:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:27:53: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 07:27:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:27:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.10_summits.bed INFO @ Fri, 26 Jun 2020 07:27:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:28:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495122/SRX495122.20_summits.bed INFO @ Fri, 26 Jun 2020 07:28:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling