Job ID = 6497440 SRX = SRX494938 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:31:04 prefetch.2.10.7: 1) Downloading 'SRR1198470'... 2020-06-25T22:31:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:36:16 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:36:16 prefetch.2.10.7: 1) 'SRR1198470' was downloaded successfully Read 24995798 spots for SRR1198470/SRR1198470.sra Written 24995798 spots for SRR1198470/SRR1198470.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: 00:06:16 24995798 reads; of these: 24995798 (100.00%) were unpaired; of these: 1672192 (6.69%) aligned 0 times 18898964 (75.61%) aligned exactly 1 time 4424642 (17.70%) aligned >1 times 93.31% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 3919045 / 23323606 = 0.1680 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 07:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.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 07:49:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:49:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:49:57: 1000000 INFO @ Fri, 26 Jun 2020 07:50:03: 2000000 INFO @ Fri, 26 Jun 2020 07:50:10: 3000000 INFO @ Fri, 26 Jun 2020 07:50:16: 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 07:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.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 07:50:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:50:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:50:22: 5000000 INFO @ Fri, 26 Jun 2020 07:50:28: 1000000 INFO @ Fri, 26 Jun 2020 07:50:29: 6000000 INFO @ Fri, 26 Jun 2020 07:50:35: 2000000 INFO @ Fri, 26 Jun 2020 07:50:36: 7000000 INFO @ Fri, 26 Jun 2020 07:50:41: 3000000 INFO @ Fri, 26 Jun 2020 07:50:43: 8000000 INFO @ Fri, 26 Jun 2020 07:50:48: 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 07:50:49: 9000000 INFO @ Fri, 26 Jun 2020 07:50:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.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 07:50:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:50:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:50:55: 5000000 INFO @ Fri, 26 Jun 2020 07:50:56: 10000000 INFO @ Fri, 26 Jun 2020 07:50:58: 1000000 INFO @ Fri, 26 Jun 2020 07:51:02: 6000000 INFO @ Fri, 26 Jun 2020 07:51:03: 11000000 INFO @ Fri, 26 Jun 2020 07:51:05: 2000000 INFO @ Fri, 26 Jun 2020 07:51:09: 7000000 INFO @ Fri, 26 Jun 2020 07:51:10: 12000000 INFO @ Fri, 26 Jun 2020 07:51:12: 3000000 INFO @ Fri, 26 Jun 2020 07:51:16: 8000000 INFO @ Fri, 26 Jun 2020 07:51:17: 13000000 INFO @ Fri, 26 Jun 2020 07:51:19: 4000000 INFO @ Fri, 26 Jun 2020 07:51:23: 9000000 INFO @ Fri, 26 Jun 2020 07:51:24: 14000000 INFO @ Fri, 26 Jun 2020 07:51:25: 5000000 INFO @ Fri, 26 Jun 2020 07:51:30: 10000000 INFO @ Fri, 26 Jun 2020 07:51:31: 15000000 INFO @ Fri, 26 Jun 2020 07:51:32: 6000000 INFO @ Fri, 26 Jun 2020 07:51:37: 11000000 INFO @ Fri, 26 Jun 2020 07:51:38: 16000000 INFO @ Fri, 26 Jun 2020 07:51:39: 7000000 INFO @ Fri, 26 Jun 2020 07:51:44: 12000000 INFO @ Fri, 26 Jun 2020 07:51:45: 17000000 INFO @ Fri, 26 Jun 2020 07:51:46: 8000000 INFO @ Fri, 26 Jun 2020 07:51:51: 13000000 INFO @ Fri, 26 Jun 2020 07:51:52: 18000000 INFO @ Fri, 26 Jun 2020 07:51:53: 9000000 INFO @ Fri, 26 Jun 2020 07:51:58: 14000000 INFO @ Fri, 26 Jun 2020 07:51:58: 19000000 INFO @ Fri, 26 Jun 2020 07:51:59: 10000000 INFO @ Fri, 26 Jun 2020 07:52:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:52:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:52:01: #1 total tags in treatment: 19404561 INFO @ Fri, 26 Jun 2020 07:52:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:01: #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 07:52:02: #1 tags after filtering in treatment: 19404561 INFO @ Fri, 26 Jun 2020 07:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:52:02: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:03: #2 number of paired peaks: 237 WARNING @ Fri, 26 Jun 2020 07:52:03: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:03: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:03: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:03: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:03: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:03: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 07:52:03: #2 alternative fragment length(s) may be 1,36,49,559 bps INFO @ Fri, 26 Jun 2020 07:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.05_model.r WARNING @ Fri, 26 Jun 2020 07:52:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:52:03: #2 You may need to consider one of the other alternative d(s): 1,36,49,559 WARNING @ Fri, 26 Jun 2020 07:52:03: #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 07:52:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:52:04: 15000000 INFO @ Fri, 26 Jun 2020 07:52:06: 11000000 INFO @ Fri, 26 Jun 2020 07:52:11: 16000000 INFO @ Fri, 26 Jun 2020 07:52:13: 12000000 INFO @ Fri, 26 Jun 2020 07:52:18: 17000000 INFO @ Fri, 26 Jun 2020 07:52:20: 13000000 INFO @ Fri, 26 Jun 2020 07:52:25: 18000000 INFO @ Fri, 26 Jun 2020 07:52:27: 14000000 INFO @ Fri, 26 Jun 2020 07:52:32: 19000000 INFO @ Fri, 26 Jun 2020 07:52:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:52:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:52:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:52:35: #1 total tags in treatment: 19404561 INFO @ Fri, 26 Jun 2020 07:52:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:35: #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 07:52:35: #1 tags after filtering in treatment: 19404561 INFO @ Fri, 26 Jun 2020 07:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:52:35: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:37: #2 number of paired peaks: 237 WARNING @ Fri, 26 Jun 2020 07:52:37: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:37: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 07:52:37: #2 alternative fragment length(s) may be 1,36,49,559 bps INFO @ Fri, 26 Jun 2020 07:52:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.10_model.r WARNING @ Fri, 26 Jun 2020 07:52:37: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:52:37: #2 You may need to consider one of the other alternative d(s): 1,36,49,559 WARNING @ Fri, 26 Jun 2020 07:52:37: #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 07:52:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:52:40: 16000000 INFO @ Fri, 26 Jun 2020 07:52:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:52:46: 17000000 INFO @ Fri, 26 Jun 2020 07:52:53: 18000000 INFO @ Fri, 26 Jun 2020 07:52:59: 19000000 INFO @ Fri, 26 Jun 2020 07:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.05_summits.bed INFO @ Fri, 26 Jun 2020 07:53:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (949 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:53:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:53:02: #1 total tags in treatment: 19404561 INFO @ Fri, 26 Jun 2020 07:53:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:02: #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 07:53:02: #1 tags after filtering in treatment: 19404561 INFO @ Fri, 26 Jun 2020 07:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:53:02: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:03: #2 number of paired peaks: 237 WARNING @ Fri, 26 Jun 2020 07:53:03: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:03: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:03: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:03: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:03: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:03: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 07:53:03: #2 alternative fragment length(s) may be 1,36,49,559 bps INFO @ Fri, 26 Jun 2020 07:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.20_model.r WARNING @ Fri, 26 Jun 2020 07:53:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:53:03: #2 You may need to consider one of the other alternative d(s): 1,36,49,559 WARNING @ Fri, 26 Jun 2020 07:53:03: #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 07:53:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.10_summits.bed INFO @ Fri, 26 Jun 2020 07:53:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494938/SRX494938.20_summits.bed INFO @ Fri, 26 Jun 2020 07:53:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 1 millis CompletedMACS2peakCalling