Job ID = 6367756 SRX = SRX4082370 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:29 prefetch.2.10.7: 1) Downloading 'SRR7164188'... 2020-06-15T23:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:34 prefetch.2.10.7: 'SRR7164188' is valid 2020-06-15T23:38:34 prefetch.2.10.7: 1) 'SRR7164188' was downloaded successfully 2020-06-15T23:38:34 prefetch.2.10.7: 'SRR7164188' has 0 unresolved dependencies Read 12607152 spots for SRR7164188/SRR7164188.sra Written 12607152 spots for SRR7164188/SRR7164188.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: 00:01:17 12607152 reads; of these: 12607152 (100.00%) were unpaired; of these: 4806697 (38.13%) aligned 0 times 5937683 (47.10%) aligned exactly 1 time 1862772 (14.78%) aligned >1 times 61.87% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 1542066 / 7800455 = 0.1977 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 08:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.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 08:42:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:19: 1000000 INFO @ Tue, 16 Jun 2020 08:42:25: 2000000 INFO @ Tue, 16 Jun 2020 08:42:30: 3000000 INFO @ Tue, 16 Jun 2020 08:42:35: 4000000 INFO @ Tue, 16 Jun 2020 08:42:40: 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 @ Tue, 16 Jun 2020 08:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.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 08:42:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:45: 6000000 INFO @ Tue, 16 Jun 2020 08:42:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:47: #1 total tags in treatment: 6258389 INFO @ Tue, 16 Jun 2020 08:42:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:47: #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 08:42:47: #1 tags after filtering in treatment: 6258389 INFO @ Tue, 16 Jun 2020 08:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:47: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:42:47: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:47: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:42:47: #2 alternative fragment length(s) may be 2,32,68,454,563,594 bps INFO @ Tue, 16 Jun 2020 08:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.05_model.r WARNING @ Tue, 16 Jun 2020 08:42:47: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:47: #2 You may need to consider one of the other alternative d(s): 2,32,68,454,563,594 WARNING @ Tue, 16 Jun 2020 08:42:47: #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 08:42:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:50: 1000000 INFO @ Tue, 16 Jun 2020 08:42:54: 2000000 INFO @ Tue, 16 Jun 2020 08:42:59: 3000000 INFO @ Tue, 16 Jun 2020 08:43:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:04: 4000000 INFO @ Tue, 16 Jun 2020 08:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:07: Done! INFO @ Tue, 16 Jun 2020 08:43:09: 5000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (377 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:43:13: 6000000 INFO @ Tue, 16 Jun 2020 08:43:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:15: #1 total tags in treatment: 6258389 INFO @ Tue, 16 Jun 2020 08:43:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:15: #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 08:43:15: #1 tags after filtering in treatment: 6258389 INFO @ Tue, 16 Jun 2020 08:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.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 08:43:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:15: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:43:15: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:15: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:43:15: #2 alternative fragment length(s) may be 2,32,68,454,563,594 bps INFO @ Tue, 16 Jun 2020 08:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.10_model.r WARNING @ Tue, 16 Jun 2020 08:43:15: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:15: #2 You may need to consider one of the other alternative d(s): 2,32,68,454,563,594 WARNING @ Tue, 16 Jun 2020 08:43:15: #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 08:43:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:20: 1000000 INFO @ Tue, 16 Jun 2020 08:43:24: 2000000 INFO @ Tue, 16 Jun 2020 08:43:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:29: 3000000 INFO @ Tue, 16 Jun 2020 08:43:34: 4000000 INFO @ Tue, 16 Jun 2020 08:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.10_summits.bed INFO @ Tue, 16 Jun 2020 08:43:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:38: 5000000 INFO @ Tue, 16 Jun 2020 08:43:43: 6000000 INFO @ Tue, 16 Jun 2020 08:43:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:44: #1 total tags in treatment: 6258389 INFO @ Tue, 16 Jun 2020 08:43:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:44: #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 08:43:44: #1 tags after filtering in treatment: 6258389 INFO @ Tue, 16 Jun 2020 08:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:45: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:43:45: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:45: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:43:45: #2 alternative fragment length(s) may be 2,32,68,454,563,594 bps INFO @ Tue, 16 Jun 2020 08:43:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.20_model.r WARNING @ Tue, 16 Jun 2020 08:43:45: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:45: #2 You may need to consider one of the other alternative d(s): 2,32,68,454,563,594 WARNING @ Tue, 16 Jun 2020 08:43:45: #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 08:43:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:45: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082370/SRX4082370.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 1 millis CompletedMACS2peakCalling