Job ID = 6507898 SRX = SRX494996 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:05:53 prefetch.2.10.7: 1) Downloading 'SRR1198528'... 2020-06-26T14:05:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:07:21 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:07:21 prefetch.2.10.7: 1) 'SRR1198528' was downloaded successfully Read 17534405 spots for SRR1198528/SRR1198528.sra Written 17534405 spots for SRR1198528/SRR1198528.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: 00:03:25 17534405 reads; of these: 17534405 (100.00%) were unpaired; of these: 8488004 (48.41%) aligned 0 times 7463003 (42.56%) aligned exactly 1 time 1583398 (9.03%) aligned >1 times 51.59% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 3299147 / 9046401 = 0.3647 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 23:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.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 23:15:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:15:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:15:14: 1000000 INFO @ Fri, 26 Jun 2020 23:15:21: 2000000 INFO @ Fri, 26 Jun 2020 23:15:28: 3000000 INFO @ Fri, 26 Jun 2020 23:15:34: 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 23:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.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 23:15:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:15:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:15:40: 5000000 INFO @ Fri, 26 Jun 2020 23:15:45: 1000000 INFO @ Fri, 26 Jun 2020 23:15:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:15:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:15:45: #1 total tags in treatment: 5747254 INFO @ Fri, 26 Jun 2020 23:15:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:45: #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 23:15:45: #1 tags after filtering in treatment: 5747254 INFO @ Fri, 26 Jun 2020 23:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:45: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:15:46: #2 number of paired peaks: 476 WARNING @ Fri, 26 Jun 2020 23:15:46: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Fri, 26 Jun 2020 23:15:46: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:46: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:46: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:46: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:46: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 23:15:46: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 26 Jun 2020 23:15:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.05_model.r WARNING @ Fri, 26 Jun 2020 23:15:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:15:46: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 26 Jun 2020 23:15:46: #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 23:15:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:51: 2000000 INFO @ Fri, 26 Jun 2020 23:15:58: 3000000 INFO @ Fri, 26 Jun 2020 23:15:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.05_summits.bed INFO @ Fri, 26 Jun 2020 23:16:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (689 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:16:04: 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 23:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.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 23:16:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:16:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:16:11: 5000000 INFO @ Fri, 26 Jun 2020 23:16:15: 1000000 INFO @ Fri, 26 Jun 2020 23:16:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:16:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:16:17: #1 total tags in treatment: 5747254 INFO @ Fri, 26 Jun 2020 23:16:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:16:17: #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 23:16:17: #1 tags after filtering in treatment: 5747254 INFO @ Fri, 26 Jun 2020 23:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:16:17: #1 finished! INFO @ Fri, 26 Jun 2020 23:16:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:16:18: #2 number of paired peaks: 476 WARNING @ Fri, 26 Jun 2020 23:16:18: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Fri, 26 Jun 2020 23:16:18: start model_add_line... INFO @ Fri, 26 Jun 2020 23:16:18: start X-correlation... INFO @ Fri, 26 Jun 2020 23:16:18: end of X-cor INFO @ Fri, 26 Jun 2020 23:16:18: #2 finished! INFO @ Fri, 26 Jun 2020 23:16:18: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 23:16:18: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 26 Jun 2020 23:16:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.10_model.r WARNING @ Fri, 26 Jun 2020 23:16:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:16:18: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 26 Jun 2020 23:16:18: #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 23:16:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:16:22: 2000000 INFO @ Fri, 26 Jun 2020 23:16:29: 3000000 INFO @ Fri, 26 Jun 2020 23:16:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.10_summits.bed INFO @ Fri, 26 Jun 2020 23:16:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:16:35: 4000000 INFO @ Fri, 26 Jun 2020 23:16:41: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:16:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:16:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:16:46: #1 total tags in treatment: 5747254 INFO @ Fri, 26 Jun 2020 23:16:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:16:46: #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 23:16:46: #1 tags after filtering in treatment: 5747254 INFO @ Fri, 26 Jun 2020 23:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:16:46: #1 finished! INFO @ Fri, 26 Jun 2020 23:16:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:16:47: #2 number of paired peaks: 476 WARNING @ Fri, 26 Jun 2020 23:16:47: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Fri, 26 Jun 2020 23:16:47: start model_add_line... INFO @ Fri, 26 Jun 2020 23:16:47: start X-correlation... INFO @ Fri, 26 Jun 2020 23:16:47: end of X-cor INFO @ Fri, 26 Jun 2020 23:16:47: #2 finished! INFO @ Fri, 26 Jun 2020 23:16:47: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 23:16:47: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 26 Jun 2020 23:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.20_model.r WARNING @ Fri, 26 Jun 2020 23:16:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:16:47: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 26 Jun 2020 23:16:47: #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 23:16:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:16:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494996/SRX494996.20_summits.bed INFO @ Fri, 26 Jun 2020 23:17:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling