Job ID = 6497491 SRX = SRX495012 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:35:05 prefetch.2.10.7: 1) Downloading 'SRR1198544'... 2020-06-25T21:35:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:37:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:37:48 prefetch.2.10.7: 1) 'SRR1198544' was downloaded successfully Read 12429446 spots for SRR1198544/SRR1198544.sra Written 12429446 spots for SRR1198544/SRR1198544.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: 00:02:22 12429446 reads; of these: 12429446 (100.00%) were unpaired; of these: 3018152 (24.28%) aligned 0 times 7926715 (63.77%) aligned exactly 1 time 1484579 (11.94%) aligned >1 times 75.72% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 5537845 / 9411294 = 0.5884 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 06:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.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 06:43:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:43:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:43:39: 1000000 INFO @ Fri, 26 Jun 2020 06:43:45: 2000000 INFO @ Fri, 26 Jun 2020 06:43:51: 3000000 INFO @ Fri, 26 Jun 2020 06:43:55: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:43:55: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:43:55: #1 total tags in treatment: 3873449 INFO @ Fri, 26 Jun 2020 06:43:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:43:55: #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 06:43:56: #1 tags after filtering in treatment: 3873449 INFO @ Fri, 26 Jun 2020 06:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:43:56: #1 finished! INFO @ Fri, 26 Jun 2020 06:43:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:43:56: #2 number of paired peaks: 625 WARNING @ Fri, 26 Jun 2020 06:43:56: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Fri, 26 Jun 2020 06:43:56: start model_add_line... INFO @ Fri, 26 Jun 2020 06:43:56: start X-correlation... INFO @ Fri, 26 Jun 2020 06:43:56: end of X-cor INFO @ Fri, 26 Jun 2020 06:43:56: #2 finished! INFO @ Fri, 26 Jun 2020 06:43:56: #2 predicted fragment length is 51 bps INFO @ Fri, 26 Jun 2020 06:43:56: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 26 Jun 2020 06:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.05_model.r WARNING @ Fri, 26 Jun 2020 06:43:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:43:56: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 26 Jun 2020 06:43:56: #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 06:43:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:43:56: #3 Pre-compute pvalue-qvalue table... 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 06:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.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 06:44:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:44:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:44:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:44:08: 1000000 INFO @ Fri, 26 Jun 2020 06:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.05_summits.bed INFO @ Fri, 26 Jun 2020 06:44:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (666 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:44:14: 2000000 INFO @ Fri, 26 Jun 2020 06:44:20: 3000000 INFO @ Fri, 26 Jun 2020 06:44:25: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:44:25: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:44:25: #1 total tags in treatment: 3873449 INFO @ Fri, 26 Jun 2020 06:44:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:44:25: #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 06:44:25: #1 tags after filtering in treatment: 3873449 INFO @ Fri, 26 Jun 2020 06:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:44:25: #1 finished! INFO @ Fri, 26 Jun 2020 06:44:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:44:25: #2 number of paired peaks: 625 WARNING @ Fri, 26 Jun 2020 06:44:25: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Fri, 26 Jun 2020 06:44:25: start model_add_line... INFO @ Fri, 26 Jun 2020 06:44:25: start X-correlation... INFO @ Fri, 26 Jun 2020 06:44:25: end of X-cor INFO @ Fri, 26 Jun 2020 06:44:25: #2 finished! INFO @ Fri, 26 Jun 2020 06:44:25: #2 predicted fragment length is 51 bps INFO @ Fri, 26 Jun 2020 06:44:25: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 26 Jun 2020 06:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.10_model.r WARNING @ Fri, 26 Jun 2020 06:44:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:44:25: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 26 Jun 2020 06:44:25: #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 06:44:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:44:25: #3 Pre-compute pvalue-qvalue table... 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 06:44:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.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 06:44:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:44:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.10_summits.bed INFO @ Fri, 26 Jun 2020 06:44:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:44:42: 1000000 INFO @ Fri, 26 Jun 2020 06:44:47: 2000000 INFO @ Fri, 26 Jun 2020 06:44:53: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:44:58: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:44:58: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:44:58: #1 total tags in treatment: 3873449 INFO @ Fri, 26 Jun 2020 06:44:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:44:58: #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 06:44:58: #1 tags after filtering in treatment: 3873449 INFO @ Fri, 26 Jun 2020 06:44:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:44:58: #1 finished! INFO @ Fri, 26 Jun 2020 06:44:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:44:59: #2 number of paired peaks: 625 WARNING @ Fri, 26 Jun 2020 06:44:59: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Fri, 26 Jun 2020 06:44:59: start model_add_line... INFO @ Fri, 26 Jun 2020 06:44:59: start X-correlation... INFO @ Fri, 26 Jun 2020 06:44:59: end of X-cor INFO @ Fri, 26 Jun 2020 06:44:59: #2 finished! INFO @ Fri, 26 Jun 2020 06:44:59: #2 predicted fragment length is 51 bps INFO @ Fri, 26 Jun 2020 06:44:59: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 26 Jun 2020 06:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.20_model.r WARNING @ Fri, 26 Jun 2020 06:44:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:44:59: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 26 Jun 2020 06:44:59: #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 06:44:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:44:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:45:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495012/SRX495012.20_summits.bed INFO @ Fri, 26 Jun 2020 06:45:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 2 millis CompletedMACS2peakCalling