Job ID = 6507812 SRX = SRX466548 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:23:29 prefetch.2.10.7: 1) Downloading 'SRR1163614'... 2020-06-26T13:23:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:26:58 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:26:58 prefetch.2.10.7: 1) 'SRR1163614' was downloaded successfully Read 21509609 spots for SRR1163614/SRR1163614.sra Written 21509609 spots for SRR1163614/SRR1163614.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: 00:03:57 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255418 (1.19%) aligned 0 times 17821601 (82.85%) aligned exactly 1 time 3432590 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 3667596 / 21254191 = 0.1726 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 22:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.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 22:37:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:11: 1000000 INFO @ Fri, 26 Jun 2020 22:37:15: 2000000 INFO @ Fri, 26 Jun 2020 22:37:20: 3000000 INFO @ Fri, 26 Jun 2020 22:37:25: 4000000 INFO @ Fri, 26 Jun 2020 22:37:30: 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 @ Fri, 26 Jun 2020 22:37:34: 6000000 INFO @ Fri, 26 Jun 2020 22:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.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 22:37:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:39: 7000000 INFO @ Fri, 26 Jun 2020 22:37:41: 1000000 INFO @ Fri, 26 Jun 2020 22:37:44: 8000000 INFO @ Fri, 26 Jun 2020 22:37:45: 2000000 INFO @ Fri, 26 Jun 2020 22:37:49: 9000000 INFO @ Fri, 26 Jun 2020 22:37:50: 3000000 INFO @ Fri, 26 Jun 2020 22:37:53: 10000000 INFO @ Fri, 26 Jun 2020 22:37:55: 4000000 INFO @ Fri, 26 Jun 2020 22:37:58: 11000000 INFO @ Fri, 26 Jun 2020 22:38:00: 5000000 INFO @ Fri, 26 Jun 2020 22:38:03: 12000000 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 22:38:05: 6000000 INFO @ Fri, 26 Jun 2020 22:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.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 22:38:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:38:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:38:08: 13000000 INFO @ Fri, 26 Jun 2020 22:38:10: 7000000 INFO @ Fri, 26 Jun 2020 22:38:11: 1000000 INFO @ Fri, 26 Jun 2020 22:38:13: 14000000 INFO @ Fri, 26 Jun 2020 22:38:14: 8000000 INFO @ Fri, 26 Jun 2020 22:38:16: 2000000 INFO @ Fri, 26 Jun 2020 22:38:18: 15000000 INFO @ Fri, 26 Jun 2020 22:38:19: 9000000 INFO @ Fri, 26 Jun 2020 22:38:21: 3000000 INFO @ Fri, 26 Jun 2020 22:38:23: 16000000 INFO @ Fri, 26 Jun 2020 22:38:24: 10000000 INFO @ Fri, 26 Jun 2020 22:38:26: 4000000 INFO @ Fri, 26 Jun 2020 22:38:28: 17000000 INFO @ Fri, 26 Jun 2020 22:38:29: 11000000 INFO @ Fri, 26 Jun 2020 22:38:30: 5000000 INFO @ Fri, 26 Jun 2020 22:38:31: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:38:31: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:38:31: #1 total tags in treatment: 17586595 INFO @ Fri, 26 Jun 2020 22:38:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:31: #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 22:38:31: #1 tags after filtering in treatment: 17586595 INFO @ Fri, 26 Jun 2020 22:38:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:31: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:32: #2 number of paired peaks: 211 WARNING @ Fri, 26 Jun 2020 22:38:32: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:32: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:32: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:32: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:32: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:38:32: #2 alternative fragment length(s) may be 1,19,588 bps INFO @ Fri, 26 Jun 2020 22:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.05_model.r WARNING @ Fri, 26 Jun 2020 22:38:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:32: #2 You may need to consider one of the other alternative d(s): 1,19,588 WARNING @ Fri, 26 Jun 2020 22:38:32: #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 22:38:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:34: 12000000 INFO @ Fri, 26 Jun 2020 22:38:35: 6000000 INFO @ Fri, 26 Jun 2020 22:38:39: 13000000 INFO @ Fri, 26 Jun 2020 22:38:40: 7000000 INFO @ Fri, 26 Jun 2020 22:38:43: 14000000 INFO @ Fri, 26 Jun 2020 22:38:45: 8000000 INFO @ Fri, 26 Jun 2020 22:38:48: 15000000 INFO @ Fri, 26 Jun 2020 22:38:49: 9000000 INFO @ Fri, 26 Jun 2020 22:38:53: 16000000 INFO @ Fri, 26 Jun 2020 22:38:54: 10000000 INFO @ Fri, 26 Jun 2020 22:38:58: 17000000 INFO @ Fri, 26 Jun 2020 22:38:59: 11000000 INFO @ Fri, 26 Jun 2020 22:39:01: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:39:01: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:39:01: #1 total tags in treatment: 17586595 INFO @ Fri, 26 Jun 2020 22:39:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:01: #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 22:39:01: #1 tags after filtering in treatment: 17586595 INFO @ Fri, 26 Jun 2020 22:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:02: #2 number of paired peaks: 211 WARNING @ Fri, 26 Jun 2020 22:39:02: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:02: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:39:02: #2 alternative fragment length(s) may be 1,19,588 bps INFO @ Fri, 26 Jun 2020 22:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.10_model.r WARNING @ Fri, 26 Jun 2020 22:39:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:02: #2 You may need to consider one of the other alternative d(s): 1,19,588 WARNING @ Fri, 26 Jun 2020 22:39:02: #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 22:39:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:04: 12000000 INFO @ Fri, 26 Jun 2020 22:39:09: 13000000 INFO @ Fri, 26 Jun 2020 22:39:14: 14000000 INFO @ Fri, 26 Jun 2020 22:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.05_summits.bed INFO @ Fri, 26 Jun 2020 22:39:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:39:18: 15000000 INFO @ Fri, 26 Jun 2020 22:39:23: 16000000 INFO @ Fri, 26 Jun 2020 22:39:28: 17000000 INFO @ Fri, 26 Jun 2020 22:39:31: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:39:31: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:39:31: #1 total tags in treatment: 17586595 INFO @ Fri, 26 Jun 2020 22:39:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:31: #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 22:39:31: #1 tags after filtering in treatment: 17586595 INFO @ Fri, 26 Jun 2020 22:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:31: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:32: #2 number of paired peaks: 211 WARNING @ Fri, 26 Jun 2020 22:39:32: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:32: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:33: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:33: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:33: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:33: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:39:33: #2 alternative fragment length(s) may be 1,19,588 bps INFO @ Fri, 26 Jun 2020 22:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.20_model.r WARNING @ Fri, 26 Jun 2020 22:39:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:33: #2 You may need to consider one of the other alternative d(s): 1,19,588 WARNING @ Fri, 26 Jun 2020 22:39:33: #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 22:39:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:39:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.10_summits.bed INFO @ Fri, 26 Jun 2020 22:39:47: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:40:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:40:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:40:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:40:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466548/SRX466548.20_summits.bed INFO @ Fri, 26 Jun 2020 22:40:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。