Job ID = 6368230 SRX = SRX494913 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:03 prefetch.2.10.7: 1) Downloading 'SRR1198445'... 2020-06-16T00:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:43 prefetch.2.10.7: 1) 'SRR1198445' was downloaded successfully Read 29666016 spots for SRR1198445/SRR1198445.sra Written 29666016 spots for SRR1198445/SRR1198445.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: 00:06:23 29666016 reads; of these: 29666016 (100.00%) were unpaired; of these: 2181881 (7.35%) aligned 0 times 22672046 (76.42%) aligned exactly 1 time 4812089 (16.22%) aligned >1 times 92.65% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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 12 files... [bam_rmdupse_core] 17077650 / 27484135 = 0.6214 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 @ Tue, 16 Jun 2020 09:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.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 @ Tue, 16 Jun 2020 09:40:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:37: 1000000 INFO @ Tue, 16 Jun 2020 09:40:42: 2000000 INFO @ Tue, 16 Jun 2020 09:40:48: 3000000 INFO @ Tue, 16 Jun 2020 09:40:53: 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 @ Tue, 16 Jun 2020 09:40:59: 5000000 INFO @ Tue, 16 Jun 2020 09:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.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 @ Tue, 16 Jun 2020 09:41:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:06: 6000000 INFO @ Tue, 16 Jun 2020 09:41:07: 1000000 INFO @ Tue, 16 Jun 2020 09:41:12: 7000000 INFO @ Tue, 16 Jun 2020 09:41:13: 2000000 INFO @ Tue, 16 Jun 2020 09:41:18: 8000000 INFO @ Tue, 16 Jun 2020 09:41:19: 3000000 INFO @ Tue, 16 Jun 2020 09:41:24: 9000000 INFO @ Tue, 16 Jun 2020 09:41:26: 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 @ Tue, 16 Jun 2020 09:41:31: 10000000 INFO @ Tue, 16 Jun 2020 09:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.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 @ Tue, 16 Jun 2020 09:41:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:32: 5000000 INFO @ Tue, 16 Jun 2020 09:41:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:33: #1 total tags in treatment: 10406485 INFO @ Tue, 16 Jun 2020 09:41:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:41:33: #1 tags after filtering in treatment: 10406485 INFO @ Tue, 16 Jun 2020 09:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:34: #2 number of paired peaks: 754 WARNING @ Tue, 16 Jun 2020 09:41:34: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:34: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:41:34: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 16 Jun 2020 09:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:34: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:34: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 16 Jun 2020 09:41:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:41:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:37: 1000000 INFO @ Tue, 16 Jun 2020 09:41:38: 6000000 INFO @ Tue, 16 Jun 2020 09:41:42: 2000000 INFO @ Tue, 16 Jun 2020 09:41:44: 7000000 INFO @ Tue, 16 Jun 2020 09:41:47: 3000000 INFO @ Tue, 16 Jun 2020 09:41:51: 8000000 INFO @ Tue, 16 Jun 2020 09:41:52: 4000000 INFO @ Tue, 16 Jun 2020 09:41:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:57: 5000000 INFO @ Tue, 16 Jun 2020 09:41:57: 9000000 INFO @ Tue, 16 Jun 2020 09:42:02: 6000000 INFO @ Tue, 16 Jun 2020 09:42:03: 10000000 INFO @ Tue, 16 Jun 2020 09:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1709 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:06: #1 total tags in treatment: 10406485 INFO @ Tue, 16 Jun 2020 09:42:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:42:06: #1 tags after filtering in treatment: 10406485 INFO @ Tue, 16 Jun 2020 09:42:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:07: 7000000 INFO @ Tue, 16 Jun 2020 09:42:07: #2 number of paired peaks: 754 WARNING @ Tue, 16 Jun 2020 09:42:07: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:07: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:42:07: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 16 Jun 2020 09:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.10_model.r WARNING @ Tue, 16 Jun 2020 09:42:07: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:07: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 16 Jun 2020 09:42:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:11: 8000000 INFO @ Tue, 16 Jun 2020 09:42:16: 9000000 INFO @ Tue, 16 Jun 2020 09:42:21: 10000000 INFO @ Tue, 16 Jun 2020 09:42:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:23: #1 total tags in treatment: 10406485 INFO @ Tue, 16 Jun 2020 09:42:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:42:24: #1 tags after filtering in treatment: 10406485 INFO @ Tue, 16 Jun 2020 09:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:24: #2 number of paired peaks: 754 WARNING @ Tue, 16 Jun 2020 09:42:24: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:25: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:42:25: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 16 Jun 2020 09:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:25: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:25: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 16 Jun 2020 09:42:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (939 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494913/SRX494913.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (397 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。