Job ID = 6497501 SRX = SRX495022 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:23:44 prefetch.2.10.7: 1) Downloading 'SRR1198554'... 2020-06-25T22:23:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:25:29 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:25:30 prefetch.2.10.7: 'SRR1198554' is valid 2020-06-25T22:25:30 prefetch.2.10.7: 1) 'SRR1198554' was downloaded successfully Read 13338445 spots for SRR1198554/SRR1198554.sra Written 13338445 spots for SRR1198554/SRR1198554.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: 00:02:33 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88992 (0.67%) aligned 0 times 10992352 (82.41%) aligned exactly 1 time 2257101 (16.92%) aligned >1 times 99.33% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 2113808 / 13249453 = 0.1595 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 07:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.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 07:31:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:03: 1000000 INFO @ Fri, 26 Jun 2020 07:32:09: 2000000 INFO @ Fri, 26 Jun 2020 07:32:14: 3000000 INFO @ Fri, 26 Jun 2020 07:32:20: 4000000 INFO @ Fri, 26 Jun 2020 07:32:26: 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 07:32:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.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 07:32:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:31: 6000000 INFO @ Fri, 26 Jun 2020 07:32:34: 1000000 INFO @ Fri, 26 Jun 2020 07:32:38: 7000000 INFO @ Fri, 26 Jun 2020 07:32:40: 2000000 INFO @ Fri, 26 Jun 2020 07:32:44: 8000000 INFO @ Fri, 26 Jun 2020 07:32:47: 3000000 INFO @ Fri, 26 Jun 2020 07:32:50: 9000000 INFO @ Fri, 26 Jun 2020 07:32:53: 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 07:32:56: 10000000 INFO @ Fri, 26 Jun 2020 07:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.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 07:32:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:59: 5000000 INFO @ Fri, 26 Jun 2020 07:33:02: 11000000 INFO @ Fri, 26 Jun 2020 07:33:03: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:33:03: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:33:03: #1 total tags in treatment: 11135645 INFO @ Fri, 26 Jun 2020 07:33:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:03: #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 07:33:03: #1 tags after filtering in treatment: 11135645 INFO @ Fri, 26 Jun 2020 07:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:03: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:04: 1000000 INFO @ Fri, 26 Jun 2020 07:33:04: #2 number of paired peaks: 378 WARNING @ Fri, 26 Jun 2020 07:33:04: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:04: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:04: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 07:33:04: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 07:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.05_model.r WARNING @ Fri, 26 Jun 2020 07:33:04: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:33:04: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 07:33:04: #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 07:33:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:05: 6000000 INFO @ Fri, 26 Jun 2020 07:33:10: 2000000 INFO @ Fri, 26 Jun 2020 07:33:11: 7000000 INFO @ Fri, 26 Jun 2020 07:33:16: 3000000 INFO @ Fri, 26 Jun 2020 07:33:17: 8000000 INFO @ Fri, 26 Jun 2020 07:33:22: 4000000 INFO @ Fri, 26 Jun 2020 07:33:23: 9000000 INFO @ Fri, 26 Jun 2020 07:33:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:33:28: 5000000 INFO @ Fri, 26 Jun 2020 07:33:29: 10000000 INFO @ Fri, 26 Jun 2020 07:33:34: 6000000 INFO @ Fri, 26 Jun 2020 07:33:35: 11000000 INFO @ Fri, 26 Jun 2020 07:33:36: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:33:36: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:33:36: #1 total tags in treatment: 11135645 INFO @ Fri, 26 Jun 2020 07:33:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:36: #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 07:33:36: #1 tags after filtering in treatment: 11135645 INFO @ Fri, 26 Jun 2020 07:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:36: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:37: #2 number of paired peaks: 378 WARNING @ Fri, 26 Jun 2020 07:33:37: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:37: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 07:33:37: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 07:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.10_model.r WARNING @ Fri, 26 Jun 2020 07:33:39: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:33:40: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 07:33:40: #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 07:33:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.05_summits.bed INFO @ Fri, 26 Jun 2020 07:33:40: Done! INFO @ Fri, 26 Jun 2020 07:33:40: 7000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:33:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:33:51: 9000000 INFO @ Fri, 26 Jun 2020 07:33:56: 10000000 INFO @ Fri, 26 Jun 2020 07:34:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:02: 11000000 INFO @ Fri, 26 Jun 2020 07:34:02: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:34:02: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:34:02: #1 total tags in treatment: 11135645 INFO @ Fri, 26 Jun 2020 07:34:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:02: #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 07:34:03: #1 tags after filtering in treatment: 11135645 INFO @ Fri, 26 Jun 2020 07:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:03: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:03: #2 number of paired peaks: 378 WARNING @ Fri, 26 Jun 2020 07:34:03: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:03: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:03: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:03: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:03: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:03: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 07:34:03: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 07:34:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.20_model.r WARNING @ Fri, 26 Jun 2020 07:34:03: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:34:03: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 07:34:03: #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 07:34:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.10_summits.bed INFO @ Fri, 26 Jun 2020 07:34:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495022/SRX495022.20_summits.bed INFO @ Fri, 26 Jun 2020 07:34:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling