Job ID = 6497481 SRX = SRX494982 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:24:34 prefetch.2.10.7: 1) Downloading 'SRR1198514'... 2020-06-25T21:24:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:25:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:25:49 prefetch.2.10.7: 'SRR1198514' is valid 2020-06-25T21:25:49 prefetch.2.10.7: 1) 'SRR1198514' was downloaded successfully Read 14259171 spots for SRR1198514/SRR1198514.sra Written 14259171 spots for SRR1198514/SRR1198514.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: 00:03:47 14259171 reads; of these: 14259171 (100.00%) were unpaired; of these: 70263 (0.49%) aligned 0 times 11597400 (81.33%) aligned exactly 1 time 2591508 (18.17%) aligned >1 times 99.51% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 1489575 / 14188908 = 0.1050 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 06:33:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.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 06:33:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:33:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:34:05: 1000000 INFO @ Fri, 26 Jun 2020 06:34:11: 2000000 INFO @ Fri, 26 Jun 2020 06:34:17: 3000000 INFO @ Fri, 26 Jun 2020 06:34:22: 4000000 INFO @ Fri, 26 Jun 2020 06:34:27: 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 06:34:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.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 06:34:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:34:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:34:33: 6000000 INFO @ Fri, 26 Jun 2020 06:34:36: 1000000 INFO @ Fri, 26 Jun 2020 06:34:39: 7000000 INFO @ Fri, 26 Jun 2020 06:34:42: 2000000 INFO @ Fri, 26 Jun 2020 06:34:45: 8000000 INFO @ Fri, 26 Jun 2020 06:34:49: 3000000 INFO @ Fri, 26 Jun 2020 06:34:51: 9000000 INFO @ Fri, 26 Jun 2020 06:34:55: 4000000 INFO @ Fri, 26 Jun 2020 06:34:57: 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 06:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.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 06:35:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:35:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:35:02: 5000000 INFO @ Fri, 26 Jun 2020 06:35:03: 11000000 INFO @ Fri, 26 Jun 2020 06:35:06: 1000000 INFO @ Fri, 26 Jun 2020 06:35:09: 6000000 INFO @ Fri, 26 Jun 2020 06:35:10: 12000000 INFO @ Fri, 26 Jun 2020 06:35:12: 2000000 INFO @ Fri, 26 Jun 2020 06:35:14: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 06:35:14: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 06:35:14: #1 total tags in treatment: 12699333 INFO @ Fri, 26 Jun 2020 06:35:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:35:14: #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 06:35:14: #1 tags after filtering in treatment: 12699333 INFO @ Fri, 26 Jun 2020 06:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:35:14: #1 finished! INFO @ Fri, 26 Jun 2020 06:35:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:35:15: #2 number of paired peaks: 310 WARNING @ Fri, 26 Jun 2020 06:35:15: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Fri, 26 Jun 2020 06:35:15: start model_add_line... INFO @ Fri, 26 Jun 2020 06:35:15: start X-correlation... INFO @ Fri, 26 Jun 2020 06:35:15: end of X-cor INFO @ Fri, 26 Jun 2020 06:35:15: #2 finished! INFO @ Fri, 26 Jun 2020 06:35:15: #2 predicted fragment length is 26 bps INFO @ Fri, 26 Jun 2020 06:35:15: #2 alternative fragment length(s) may be 1,26,559,585,591 bps INFO @ Fri, 26 Jun 2020 06:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.05_model.r INFO @ Fri, 26 Jun 2020 06:35:15: 7000000 WARNING @ Fri, 26 Jun 2020 06:35:18: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:35:18: #2 You may need to consider one of the other alternative d(s): 1,26,559,585,591 WARNING @ Fri, 26 Jun 2020 06:35:18: #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 06:35:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:35:18: 3000000 INFO @ Fri, 26 Jun 2020 06:35:22: 8000000 INFO @ Fri, 26 Jun 2020 06:35:24: 4000000 INFO @ Fri, 26 Jun 2020 06:35:28: 9000000 INFO @ Fri, 26 Jun 2020 06:35:30: 5000000 INFO @ Fri, 26 Jun 2020 06:35:35: 10000000 INFO @ Fri, 26 Jun 2020 06:35:36: 6000000 INFO @ Fri, 26 Jun 2020 06:35:41: 11000000 INFO @ Fri, 26 Jun 2020 06:35:42: 7000000 INFO @ Fri, 26 Jun 2020 06:35:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:35:47: 12000000 INFO @ Fri, 26 Jun 2020 06:35:47: 8000000 INFO @ Fri, 26 Jun 2020 06:35:51: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 06:35:51: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 06:35:51: #1 total tags in treatment: 12699333 INFO @ Fri, 26 Jun 2020 06:35:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:35:51: #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 06:35:51: #1 tags after filtering in treatment: 12699333 INFO @ Fri, 26 Jun 2020 06:35:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:35:51: #1 finished! INFO @ Fri, 26 Jun 2020 06:35:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:35:52: #2 number of paired peaks: 310 WARNING @ Fri, 26 Jun 2020 06:35:52: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Fri, 26 Jun 2020 06:35:52: start model_add_line... INFO @ Fri, 26 Jun 2020 06:35:52: start X-correlation... INFO @ Fri, 26 Jun 2020 06:35:52: end of X-cor INFO @ Fri, 26 Jun 2020 06:35:52: #2 finished! INFO @ Fri, 26 Jun 2020 06:35:52: #2 predicted fragment length is 26 bps INFO @ Fri, 26 Jun 2020 06:35:52: #2 alternative fragment length(s) may be 1,26,559,585,591 bps INFO @ Fri, 26 Jun 2020 06:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.10_model.r WARNING @ Fri, 26 Jun 2020 06:35:52: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:35:52: #2 You may need to consider one of the other alternative d(s): 1,26,559,585,591 WARNING @ Fri, 26 Jun 2020 06:35:52: #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 06:35:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:35:53: 9000000 INFO @ Fri, 26 Jun 2020 06:35:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.05_peaks.xls BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 06:35:59: 10000000 INFO @ Fri, 26 Jun 2020 06:36:04: 11000000 INFO @ Fri, 26 Jun 2020 06:36:10: 12000000 INFO @ Fri, 26 Jun 2020 06:36:14: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 06:36:14: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 06:36:14: #1 total tags in treatment: 12699333 INFO @ Fri, 26 Jun 2020 06:36:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:36:14: #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 06:36:14: #1 tags after filtering in treatment: 12699333 INFO @ Fri, 26 Jun 2020 06:36:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:36:14: #1 finished! INFO @ Fri, 26 Jun 2020 06:36:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:36:15: #2 number of paired peaks: 310 WARNING @ Fri, 26 Jun 2020 06:36:15: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Fri, 26 Jun 2020 06:36:15: start model_add_line... INFO @ Fri, 26 Jun 2020 06:36:15: start X-correlation... INFO @ Fri, 26 Jun 2020 06:36:15: end of X-cor INFO @ Fri, 26 Jun 2020 06:36:15: #2 finished! INFO @ Fri, 26 Jun 2020 06:36:15: #2 predicted fragment length is 26 bps INFO @ Fri, 26 Jun 2020 06:36:15: #2 alternative fragment length(s) may be 1,26,559,585,591 bps INFO @ Fri, 26 Jun 2020 06:36:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.20_model.r INFO @ Fri, 26 Jun 2020 06:36:17: #3 Call peaks for each chromosome... BigWig に変換中... WARNING @ Fri, 26 Jun 2020 06:36:20: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:36:20: #2 You may need to consider one of the other alternative d(s): 1,26,559,585,591 WARNING @ Fri, 26 Jun 2020 06:36:20: #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 06:36:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.05_summits.bed INFO @ Fri, 26 Jun 2020 06:36:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 71 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.10_summits.bed INFO @ Fri, 26 Jun 2020 06:36:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 2301 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:36:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494982/SRX494982.20_summits.bed BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:37:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (61 records, 4 fields): 97 millis CompletedMACS2peakCalling