Job ID = 6497507 SRX = SRX495097 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:00:40 prefetch.2.10.7: 1) Downloading 'SRR1198629'... 2020-06-25T22:00:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:02:25 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:02:26 prefetch.2.10.7: 'SRR1198629' is valid 2020-06-25T22:02:26 prefetch.2.10.7: 1) 'SRR1198629' was downloaded successfully Read 15351480 spots for SRR1198629/SRR1198629.sra Written 15351480 spots for SRR1198629/SRR1198629.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: 00:03:02 15351480 reads; of these: 15351480 (100.00%) were unpaired; of these: 138655 (0.90%) aligned 0 times 12384852 (80.68%) aligned exactly 1 time 2827973 (18.42%) aligned >1 times 99.10% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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_rmdupse_core] 2342149 / 15212825 = 0.1540 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 07:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.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 07:10:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:10:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:10:59: 1000000 INFO @ Fri, 26 Jun 2020 07:11:04: 2000000 INFO @ Fri, 26 Jun 2020 07:11:09: 3000000 INFO @ Fri, 26 Jun 2020 07:11:15: 4000000 INFO @ Fri, 26 Jun 2020 07:11:20: 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 07:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.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 07:11:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:11:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:11:25: 6000000 INFO @ Fri, 26 Jun 2020 07:11:29: 1000000 INFO @ Fri, 26 Jun 2020 07:11:31: 7000000 INFO @ Fri, 26 Jun 2020 07:11:34: 2000000 INFO @ Fri, 26 Jun 2020 07:11:37: 8000000 INFO @ Fri, 26 Jun 2020 07:11:40: 3000000 INFO @ Fri, 26 Jun 2020 07:11:43: 9000000 INFO @ Fri, 26 Jun 2020 07:11:46: 4000000 INFO @ Fri, 26 Jun 2020 07:11:48: 10000000 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 07:11:52: 5000000 INFO @ Fri, 26 Jun 2020 07:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.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 07:11:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:11:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:11:54: 11000000 INFO @ Fri, 26 Jun 2020 07:11:58: 6000000 INFO @ Fri, 26 Jun 2020 07:11:59: 1000000 INFO @ Fri, 26 Jun 2020 07:12:00: 12000000 INFO @ Fri, 26 Jun 2020 07:12:03: 7000000 INFO @ Fri, 26 Jun 2020 07:12:04: 2000000 INFO @ Fri, 26 Jun 2020 07:12:05: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:12:05: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:12:05: #1 total tags in treatment: 12870676 INFO @ Fri, 26 Jun 2020 07:12:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:05: #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 07:12:05: #1 tags after filtering in treatment: 12870676 INFO @ Fri, 26 Jun 2020 07:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:06: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 07:12:06: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:06: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:06: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:06: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:06: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:06: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 07:12:06: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 07:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.05_model.r WARNING @ Fri, 26 Jun 2020 07:12:07: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:07: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 07:12:07: #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 07:12:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:09: 8000000 INFO @ Fri, 26 Jun 2020 07:12:10: 3000000 INFO @ Fri, 26 Jun 2020 07:12:15: 9000000 INFO @ Fri, 26 Jun 2020 07:12:16: 4000000 INFO @ Fri, 26 Jun 2020 07:12:21: 10000000 INFO @ Fri, 26 Jun 2020 07:12:21: 5000000 INFO @ Fri, 26 Jun 2020 07:12:26: 11000000 INFO @ Fri, 26 Jun 2020 07:12:27: 6000000 INFO @ Fri, 26 Jun 2020 07:12:32: 12000000 INFO @ Fri, 26 Jun 2020 07:12:33: 7000000 INFO @ Fri, 26 Jun 2020 07:12:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:12:37: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:12:37: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:12:37: #1 total tags in treatment: 12870676 INFO @ Fri, 26 Jun 2020 07:12:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:37: #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 07:12:37: #1 tags after filtering in treatment: 12870676 INFO @ Fri, 26 Jun 2020 07:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:37: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:38: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 07:12:38: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:38: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:38: 8000000 INFO @ Fri, 26 Jun 2020 07:12:38: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:38: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:38: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:38: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 07:12:38: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 07:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.10_model.r WARNING @ Fri, 26 Jun 2020 07:12:38: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:38: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 07:12:38: #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 07:12:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:44: 9000000 INFO @ Fri, 26 Jun 2020 07:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.05_summits.bed INFO @ Fri, 26 Jun 2020 07:12:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2248 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:12:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:12:55: 11000000 INFO @ Fri, 26 Jun 2020 07:13:00: 12000000 INFO @ Fri, 26 Jun 2020 07:13:05: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:13:05: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:13:05: #1 total tags in treatment: 12870676 INFO @ Fri, 26 Jun 2020 07:13:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:13:05: #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 07:13:05: #1 tags after filtering in treatment: 12870676 INFO @ Fri, 26 Jun 2020 07:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:13:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:13:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:13:06: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 07:13:06: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 07:13:06: start model_add_line... INFO @ Fri, 26 Jun 2020 07:13:06: start X-correlation... INFO @ Fri, 26 Jun 2020 07:13:06: end of X-cor INFO @ Fri, 26 Jun 2020 07:13:06: #2 finished! INFO @ Fri, 26 Jun 2020 07:13:06: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 07:13:06: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 07:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.20_model.r WARNING @ Fri, 26 Jun 2020 07:13:06: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:13:06: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 07:13:06: #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 07:13:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:13:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.10_summits.bed INFO @ Fri, 26 Jun 2020 07:13:23: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (630 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:13:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495097/SRX495097.20_summits.bed INFO @ Fri, 26 Jun 2020 07:13:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling