Job ID = 6507881 SRX = SRX494966 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:38:41 prefetch.2.10.7: 1) Downloading 'SRR1198498'... 2020-06-26T13:38:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:41:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:41:06 prefetch.2.10.7: 'SRR1198498' is valid 2020-06-26T13:41:06 prefetch.2.10.7: 1) 'SRR1198498' was downloaded successfully Read 19040559 spots for SRR1198498/SRR1198498.sra Written 19040559 spots for SRR1198498/SRR1198498.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: 00:04:23 19040559 reads; of these: 19040559 (100.00%) were unpaired; of these: 793486 (4.17%) aligned 0 times 15280440 (80.25%) aligned exactly 1 time 2966633 (15.58%) aligned >1 times 95.83% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 10943892 / 18247073 = 0.5998 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 22:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.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 22:49:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:02: 1000000 INFO @ Fri, 26 Jun 2020 22:50:08: 2000000 INFO @ Fri, 26 Jun 2020 22:50:14: 3000000 INFO @ Fri, 26 Jun 2020 22:50:20: 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 22:50:26: 5000000 INFO @ Fri, 26 Jun 2020 22:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.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 22:50:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:32: 6000000 INFO @ Fri, 26 Jun 2020 22:50:32: 1000000 INFO @ Fri, 26 Jun 2020 22:50:38: 7000000 INFO @ Fri, 26 Jun 2020 22:50:38: 2000000 INFO @ Fri, 26 Jun 2020 22:50:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:50:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:50:40: #1 total tags in treatment: 7303181 INFO @ Fri, 26 Jun 2020 22:50:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:40: #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 22:50:40: #1 tags after filtering in treatment: 7303181 INFO @ Fri, 26 Jun 2020 22:50:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:50:40: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:41: #2 number of paired peaks: 518 WARNING @ Fri, 26 Jun 2020 22:50:41: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:41: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:41: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:41: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:41: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:41: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:50:41: #2 alternative fragment length(s) may be 3,50,557 bps INFO @ Fri, 26 Jun 2020 22:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.05_model.r WARNING @ Fri, 26 Jun 2020 22:50:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:50:41: #2 You may need to consider one of the other alternative d(s): 3,50,557 WARNING @ Fri, 26 Jun 2020 22:50:41: #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 22:50:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:50:44: 3000000 INFO @ Fri, 26 Jun 2020 22:50:50: 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 22:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.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 22:50:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:56: 5000000 INFO @ Fri, 26 Jun 2020 22:50:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:02: 1000000 INFO @ Fri, 26 Jun 2020 22:51:03: 6000000 INFO @ Fri, 26 Jun 2020 22:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.05_summits.bed INFO @ Fri, 26 Jun 2020 22:51:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (772 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:51:07: 2000000 INFO @ Fri, 26 Jun 2020 22:51:09: 7000000 INFO @ Fri, 26 Jun 2020 22:51:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:51:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:51:11: #1 total tags in treatment: 7303181 INFO @ Fri, 26 Jun 2020 22:51:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:11: #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 22:51:11: #1 tags after filtering in treatment: 7303181 INFO @ Fri, 26 Jun 2020 22:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:11: #2 number of paired peaks: 518 WARNING @ Fri, 26 Jun 2020 22:51:11: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Fri, 26 Jun 2020 22:51:11: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:11: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:11: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:11: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:11: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:51:11: #2 alternative fragment length(s) may be 3,50,557 bps INFO @ Fri, 26 Jun 2020 22:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.10_model.r WARNING @ Fri, 26 Jun 2020 22:51:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:51:11: #2 You may need to consider one of the other alternative d(s): 3,50,557 WARNING @ Fri, 26 Jun 2020 22:51:11: #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 22:51:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:51:12: 3000000 INFO @ Fri, 26 Jun 2020 22:51:17: 4000000 INFO @ Fri, 26 Jun 2020 22:51:23: 5000000 INFO @ Fri, 26 Jun 2020 22:51:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:28: 6000000 INFO @ Fri, 26 Jun 2020 22:51:33: 7000000 INFO @ Fri, 26 Jun 2020 22:51:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:51:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:51:35: #1 total tags in treatment: 7303181 INFO @ Fri, 26 Jun 2020 22:51:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:35: #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 22:51:35: #1 tags after filtering in treatment: 7303181 INFO @ Fri, 26 Jun 2020 22:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:35: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:36: #2 number of paired peaks: 518 WARNING @ Fri, 26 Jun 2020 22:51:36: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Fri, 26 Jun 2020 22:51:36: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:36: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:36: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:36: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:36: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:51:36: #2 alternative fragment length(s) may be 3,50,557 bps INFO @ Fri, 26 Jun 2020 22:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.20_model.r WARNING @ Fri, 26 Jun 2020 22:51:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:51:36: #2 You may need to consider one of the other alternative d(s): 3,50,557 WARNING @ Fri, 26 Jun 2020 22:51:36: #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 22:51:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.10_summits.bed INFO @ Fri, 26 Jun 2020 22:51:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:51:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494966/SRX494966.20_summits.bed INFO @ Fri, 26 Jun 2020 22:52:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 2 millis CompletedMACS2peakCalling