Job ID = 6368613 SRX = SRX5020838 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:16 prefetch.2.10.7: 1) Downloading 'SRR8201461'... 2020-06-16T00:35:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:19 prefetch.2.10.7: 1) 'SRR8201461' was downloaded successfully Read 16440500 spots for SRR8201461/SRR8201461.sra Written 16440500 spots for SRR8201461/SRR8201461.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: 00:03:52 16440500 reads; of these: 16440500 (100.00%) were unpaired; of these: 137976 (0.84%) aligned 0 times 13513060 (82.19%) aligned exactly 1 time 2789464 (16.97%) aligned >1 times 99.16% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 1797756 / 16302524 = 0.1103 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 09:46:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.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 09:46:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:40: 1000000 INFO @ Tue, 16 Jun 2020 09:46:45: 2000000 INFO @ Tue, 16 Jun 2020 09:46:51: 3000000 INFO @ Tue, 16 Jun 2020 09:46:57: 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 @ Tue, 16 Jun 2020 09:47:03: 5000000 INFO @ Tue, 16 Jun 2020 09:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.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 09:47:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:09: 6000000 INFO @ Tue, 16 Jun 2020 09:47:09: 1000000 INFO @ Tue, 16 Jun 2020 09:47:15: 2000000 INFO @ Tue, 16 Jun 2020 09:47:15: 7000000 INFO @ Tue, 16 Jun 2020 09:47:21: 3000000 INFO @ Tue, 16 Jun 2020 09:47:21: 8000000 INFO @ Tue, 16 Jun 2020 09:47:26: 4000000 INFO @ Tue, 16 Jun 2020 09:47:27: 9000000 INFO @ Tue, 16 Jun 2020 09:47:32: 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 @ Tue, 16 Jun 2020 09:47:33: 10000000 INFO @ Tue, 16 Jun 2020 09:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.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 09:47:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:37: 6000000 INFO @ Tue, 16 Jun 2020 09:47:40: 11000000 INFO @ Tue, 16 Jun 2020 09:47:40: 1000000 INFO @ Tue, 16 Jun 2020 09:47:43: 7000000 INFO @ Tue, 16 Jun 2020 09:47:46: 12000000 INFO @ Tue, 16 Jun 2020 09:47:46: 2000000 INFO @ Tue, 16 Jun 2020 09:47:49: 8000000 INFO @ Tue, 16 Jun 2020 09:47:52: 13000000 INFO @ Tue, 16 Jun 2020 09:47:53: 3000000 INFO @ Tue, 16 Jun 2020 09:47:54: 9000000 INFO @ Tue, 16 Jun 2020 09:47:58: 14000000 INFO @ Tue, 16 Jun 2020 09:47:59: 4000000 INFO @ Tue, 16 Jun 2020 09:48:00: 10000000 INFO @ Tue, 16 Jun 2020 09:48:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:01: #1 total tags in treatment: 14504768 INFO @ Tue, 16 Jun 2020 09:48:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:01: #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 09:48:02: #1 tags after filtering in treatment: 14504768 INFO @ Tue, 16 Jun 2020 09:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:03: #2 number of paired peaks: 327 WARNING @ Tue, 16 Jun 2020 09:48:03: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:03: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:48:03: #2 alternative fragment length(s) may be 2,47,574 bps INFO @ Tue, 16 Jun 2020 09:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:03: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:03: #2 You may need to consider one of the other alternative d(s): 2,47,574 WARNING @ Tue, 16 Jun 2020 09:48:03: #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 09:48:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:05: 5000000 INFO @ Tue, 16 Jun 2020 09:48:06: 11000000 INFO @ Tue, 16 Jun 2020 09:48:11: 12000000 INFO @ Tue, 16 Jun 2020 09:48:11: 6000000 INFO @ Tue, 16 Jun 2020 09:48:17: 13000000 INFO @ Tue, 16 Jun 2020 09:48:18: 7000000 INFO @ Tue, 16 Jun 2020 09:48:23: 14000000 INFO @ Tue, 16 Jun 2020 09:48:24: 8000000 INFO @ Tue, 16 Jun 2020 09:48:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:26: #1 total tags in treatment: 14504768 INFO @ Tue, 16 Jun 2020 09:48:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:26: #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 09:48:26: #1 tags after filtering in treatment: 14504768 INFO @ Tue, 16 Jun 2020 09:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:27: #2 number of paired peaks: 327 WARNING @ Tue, 16 Jun 2020 09:48:27: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:27: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:48:27: #2 alternative fragment length(s) may be 2,47,574 bps INFO @ Tue, 16 Jun 2020 09:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:27: #2 You may need to consider one of the other alternative d(s): 2,47,574 WARNING @ Tue, 16 Jun 2020 09:48:27: #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 09:48:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:30: 9000000 INFO @ Tue, 16 Jun 2020 09:48:36: 10000000 INFO @ Tue, 16 Jun 2020 09:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.05_summits.bed INFO @ Tue, 16 Jun 2020 09:48:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (707 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:42: 11000000 INFO @ Tue, 16 Jun 2020 09:48:48: 12000000 INFO @ Tue, 16 Jun 2020 09:48:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:54: 13000000 INFO @ Tue, 16 Jun 2020 09:49:01: 14000000 INFO @ Tue, 16 Jun 2020 09:49:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:04: #1 total tags in treatment: 14504768 INFO @ Tue, 16 Jun 2020 09:49:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:04: #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 09:49:04: #1 tags after filtering in treatment: 14504768 INFO @ Tue, 16 Jun 2020 09:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:05: #2 number of paired peaks: 327 WARNING @ Tue, 16 Jun 2020 09:49:05: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:06: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:49:06: #2 alternative fragment length(s) may be 2,47,574 bps INFO @ Tue, 16 Jun 2020 09:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:06: #2 You may need to consider one of the other alternative d(s): 2,47,574 WARNING @ Tue, 16 Jun 2020 09:49:06: #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 09:49:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (499 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020838/SRX5020838.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling