Job ID = 6507714 SRX = SRX059265 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:30:18 prefetch.2.10.7: 1) Downloading 'SRR190705'... 2020-06-26T13:30:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:32:02 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:32:03 prefetch.2.10.7: 'SRR190705' is valid 2020-06-26T13:32:03 prefetch.2.10.7: 1) 'SRR190705' was downloaded successfully Read 23070060 spots for SRR190705/SRR190705.sra Written 23070060 spots for SRR190705/SRR190705.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:26 23070060 reads; of these: 23070060 (100.00%) were unpaired; of these: 5699462 (24.71%) aligned 0 times 15030446 (65.15%) aligned exactly 1 time 2340152 (10.14%) aligned >1 times 75.29% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 2620991 / 17370598 = 0.1509 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 22:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.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 22:40:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:40:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:40:54: 1000000 INFO @ Fri, 26 Jun 2020 22:41:01: 2000000 INFO @ Fri, 26 Jun 2020 22:41:07: 3000000 INFO @ Fri, 26 Jun 2020 22:41:14: 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 22:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.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 22:41:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:41:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:41:21: 5000000 INFO @ Fri, 26 Jun 2020 22:41:25: 1000000 INFO @ Fri, 26 Jun 2020 22:41:28: 6000000 INFO @ Fri, 26 Jun 2020 22:41:32: 2000000 INFO @ Fri, 26 Jun 2020 22:41:35: 7000000 INFO @ Fri, 26 Jun 2020 22:41:39: 3000000 INFO @ Fri, 26 Jun 2020 22:41:42: 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 @ Fri, 26 Jun 2020 22:41:46: 4000000 INFO @ Fri, 26 Jun 2020 22:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.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 22:41:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:41:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:41:49: 9000000 INFO @ Fri, 26 Jun 2020 22:41:54: 5000000 INFO @ Fri, 26 Jun 2020 22:41:55: 1000000 INFO @ Fri, 26 Jun 2020 22:41:56: 10000000 INFO @ Fri, 26 Jun 2020 22:42:00: 6000000 INFO @ Fri, 26 Jun 2020 22:42:02: 2000000 INFO @ Fri, 26 Jun 2020 22:42:04: 11000000 INFO @ Fri, 26 Jun 2020 22:42:07: 7000000 INFO @ Fri, 26 Jun 2020 22:42:09: 3000000 INFO @ Fri, 26 Jun 2020 22:42:11: 12000000 INFO @ Fri, 26 Jun 2020 22:42:14: 8000000 INFO @ Fri, 26 Jun 2020 22:42:16: 4000000 INFO @ Fri, 26 Jun 2020 22:42:19: 13000000 INFO @ Fri, 26 Jun 2020 22:42:21: 9000000 INFO @ Fri, 26 Jun 2020 22:42:23: 5000000 INFO @ Fri, 26 Jun 2020 22:42:26: 14000000 INFO @ Fri, 26 Jun 2020 22:42:28: 10000000 INFO @ Fri, 26 Jun 2020 22:42:30: 6000000 INFO @ Fri, 26 Jun 2020 22:42:32: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:42:32: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:42:32: #1 total tags in treatment: 14749607 INFO @ Fri, 26 Jun 2020 22:42:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:42:32: #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 22:42:32: #1 tags after filtering in treatment: 14749607 INFO @ Fri, 26 Jun 2020 22:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:42:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:42:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:42:33: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 22:42:33: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 22:42:33: start model_add_line... INFO @ Fri, 26 Jun 2020 22:42:33: start X-correlation... INFO @ Fri, 26 Jun 2020 22:42:33: end of X-cor INFO @ Fri, 26 Jun 2020 22:42:33: #2 finished! INFO @ Fri, 26 Jun 2020 22:42:33: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 22:42:33: #2 alternative fragment length(s) may be 2,31,61,484,507,537,598 bps INFO @ Fri, 26 Jun 2020 22:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.05_model.r WARNING @ Fri, 26 Jun 2020 22:42:33: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:42:33: #2 You may need to consider one of the other alternative d(s): 2,31,61,484,507,537,598 WARNING @ Fri, 26 Jun 2020 22:42:33: #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 22:42:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:42:35: 11000000 INFO @ Fri, 26 Jun 2020 22:42:37: 7000000 INFO @ Fri, 26 Jun 2020 22:42:42: 12000000 INFO @ Fri, 26 Jun 2020 22:42:44: 8000000 INFO @ Fri, 26 Jun 2020 22:42:49: 13000000 INFO @ Fri, 26 Jun 2020 22:42:50: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:42:56: 14000000 INFO @ Fri, 26 Jun 2020 22:42:57: 10000000 INFO @ Fri, 26 Jun 2020 22:43:01: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:43:01: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:43:01: #1 total tags in treatment: 14749607 INFO @ Fri, 26 Jun 2020 22:43:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:43:01: #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 22:43:01: #1 tags after filtering in treatment: 14749607 INFO @ Fri, 26 Jun 2020 22:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:43:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:43:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:43:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:43:02: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 22:43:02: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 22:43:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:43:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:43:03: end of X-cor INFO @ Fri, 26 Jun 2020 22:43:03: #2 finished! INFO @ Fri, 26 Jun 2020 22:43:03: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 22:43:03: #2 alternative fragment length(s) may be 2,31,61,484,507,537,598 bps INFO @ Fri, 26 Jun 2020 22:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.10_model.r WARNING @ Fri, 26 Jun 2020 22:43:03: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:43:03: #2 You may need to consider one of the other alternative d(s): 2,31,61,484,507,537,598 WARNING @ Fri, 26 Jun 2020 22:43:03: #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 22:43:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:43:04: 11000000 INFO @ Fri, 26 Jun 2020 22:43:11: 12000000 INFO @ Fri, 26 Jun 2020 22:43:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:43:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:43:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.05_summits.bed INFO @ Fri, 26 Jun 2020 22:43:15: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:43:17: 13000000 INFO @ Fri, 26 Jun 2020 22:43:24: 14000000 INFO @ Fri, 26 Jun 2020 22:43:29: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:43:29: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:43:29: #1 total tags in treatment: 14749607 INFO @ Fri, 26 Jun 2020 22:43:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:43:29: #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 22:43:29: #1 tags after filtering in treatment: 14749607 INFO @ Fri, 26 Jun 2020 22:43:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:43:29: #1 finished! INFO @ Fri, 26 Jun 2020 22:43:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:43:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:43:30: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 22:43:30: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 22:43:30: start model_add_line... INFO @ Fri, 26 Jun 2020 22:43:30: start X-correlation... INFO @ Fri, 26 Jun 2020 22:43:30: end of X-cor INFO @ Fri, 26 Jun 2020 22:43:30: #2 finished! INFO @ Fri, 26 Jun 2020 22:43:30: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 22:43:30: #2 alternative fragment length(s) may be 2,31,61,484,507,537,598 bps INFO @ Fri, 26 Jun 2020 22:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.20_model.r WARNING @ Fri, 26 Jun 2020 22:43:30: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:43:30: #2 You may need to consider one of the other alternative d(s): 2,31,61,484,507,537,598 WARNING @ Fri, 26 Jun 2020 22:43:30: #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 22:43:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:43:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:43:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:43:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:43:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.10_summits.bed INFO @ Fri, 26 Jun 2020 22:43:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:43:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059265/SRX059265.20_summits.bed INFO @ Fri, 26 Jun 2020 22:44:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling