Job ID = 6497492 SRX = SRX495013 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:22:31 prefetch.2.10.7: 1) Downloading 'SRR1198545'... 2020-06-25T22:22:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:24:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:24:44 prefetch.2.10.7: 'SRR1198545' is valid 2020-06-25T22:24:44 prefetch.2.10.7: 1) 'SRR1198545' was downloaded successfully Read 18854814 spots for SRR1198545/SRR1198545.sra Written 18854814 spots for SRR1198545/SRR1198545.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: 00:03:29 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289152 (1.53%) aligned 0 times 14953772 (79.31%) aligned exactly 1 time 3611890 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 3522107 / 18565662 = 0.1897 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 07:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.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 07:33:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:29: 1000000 INFO @ Fri, 26 Jun 2020 07:33:34: 2000000 INFO @ Fri, 26 Jun 2020 07:33:39: 3000000 INFO @ Fri, 26 Jun 2020 07:33:43: 4000000 INFO @ Fri, 26 Jun 2020 07:33:48: 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 07:33:52: 6000000 INFO @ Fri, 26 Jun 2020 07:33:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.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 07:33:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:57: 7000000 INFO @ Fri, 26 Jun 2020 07:33:58: 1000000 INFO @ Fri, 26 Jun 2020 07:34:02: 8000000 INFO @ Fri, 26 Jun 2020 07:34:02: 2000000 INFO @ Fri, 26 Jun 2020 07:34:07: 9000000 INFO @ Fri, 26 Jun 2020 07:34:07: 3000000 INFO @ Fri, 26 Jun 2020 07:34:11: 10000000 INFO @ Fri, 26 Jun 2020 07:34:12: 4000000 INFO @ Fri, 26 Jun 2020 07:34:16: 11000000 INFO @ Fri, 26 Jun 2020 07:34:17: 5000000 INFO @ Fri, 26 Jun 2020 07:34:21: 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 07:34:21: 6000000 INFO @ Fri, 26 Jun 2020 07:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.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 07:34:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:25: 13000000 INFO @ Fri, 26 Jun 2020 07:34:26: 7000000 INFO @ Fri, 26 Jun 2020 07:34:28: 1000000 INFO @ Fri, 26 Jun 2020 07:34:30: 14000000 INFO @ Fri, 26 Jun 2020 07:34:31: 8000000 INFO @ Fri, 26 Jun 2020 07:34:33: 2000000 INFO @ Fri, 26 Jun 2020 07:34:35: 15000000 INFO @ Fri, 26 Jun 2020 07:34:35: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:34:35: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:34:35: #1 total tags in treatment: 15043555 INFO @ Fri, 26 Jun 2020 07:34:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:35: #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 07:34:36: #1 tags after filtering in treatment: 15043555 INFO @ Fri, 26 Jun 2020 07:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:36: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:36: 9000000 INFO @ Fri, 26 Jun 2020 07:34:37: #2 number of paired peaks: 431 WARNING @ Fri, 26 Jun 2020 07:34:37: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:37: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:34:37: #2 alternative fragment length(s) may be 2,45 bps INFO @ Fri, 26 Jun 2020 07:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.05_model.r WARNING @ Fri, 26 Jun 2020 07:34:37: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:34:37: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Fri, 26 Jun 2020 07:34:37: #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 07:34:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:37: 3000000 INFO @ Fri, 26 Jun 2020 07:34:40: 10000000 INFO @ Fri, 26 Jun 2020 07:34:42: 4000000 INFO @ Fri, 26 Jun 2020 07:34:45: 11000000 INFO @ Fri, 26 Jun 2020 07:34:47: 5000000 INFO @ Fri, 26 Jun 2020 07:34:50: 12000000 INFO @ Fri, 26 Jun 2020 07:34:52: 6000000 INFO @ Fri, 26 Jun 2020 07:34:55: 13000000 INFO @ Fri, 26 Jun 2020 07:34:57: 7000000 INFO @ Fri, 26 Jun 2020 07:34:59: 14000000 INFO @ Fri, 26 Jun 2020 07:35:01: 8000000 INFO @ Fri, 26 Jun 2020 07:35:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:04: 15000000 INFO @ Fri, 26 Jun 2020 07:35:04: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:35:04: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:35:04: #1 total tags in treatment: 15043555 INFO @ Fri, 26 Jun 2020 07:35:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:04: #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 07:35:04: #1 tags after filtering in treatment: 15043555 INFO @ Fri, 26 Jun 2020 07:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:04: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:05: #2 number of paired peaks: 431 WARNING @ Fri, 26 Jun 2020 07:35:05: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:05: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:05: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:05: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:05: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:05: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:35:05: #2 alternative fragment length(s) may be 2,45 bps INFO @ Fri, 26 Jun 2020 07:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.10_model.r WARNING @ Fri, 26 Jun 2020 07:35:06: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:35:06: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Fri, 26 Jun 2020 07:35:06: #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 07:35:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:35:06: 9000000 INFO @ Fri, 26 Jun 2020 07:35:11: 10000000 INFO @ Fri, 26 Jun 2020 07:35:15: 11000000 INFO @ Fri, 26 Jun 2020 07:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.05_summits.bed INFO @ Fri, 26 Jun 2020 07:35:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3853 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:20: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:35:25: 13000000 INFO @ Fri, 26 Jun 2020 07:35:29: 14000000 INFO @ Fri, 26 Jun 2020 07:35:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:34: 15000000 INFO @ Fri, 26 Jun 2020 07:35:34: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:35:34: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:35:34: #1 total tags in treatment: 15043555 INFO @ Fri, 26 Jun 2020 07:35:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:34: #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 07:35:34: #1 tags after filtering in treatment: 15043555 INFO @ Fri, 26 Jun 2020 07:35:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:34: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:35: #2 number of paired peaks: 431 WARNING @ Fri, 26 Jun 2020 07:35:35: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:36: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:36: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:36: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:36: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:35:36: #2 alternative fragment length(s) may be 2,45 bps INFO @ Fri, 26 Jun 2020 07:35:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.20_model.r WARNING @ Fri, 26 Jun 2020 07:35:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:35:36: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Fri, 26 Jun 2020 07:35:36: #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 07:35:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.10_summits.bed INFO @ Fri, 26 Jun 2020 07:35:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (939 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:36:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495013/SRX495013.20_summits.bed INFO @ Fri, 26 Jun 2020 07:36:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling