Job ID = 6529113 SRX = SRX5709763 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:03 27893567 reads; of these: 27893567 (100.00%) were unpaired; of these: 5336084 (19.13%) aligned 0 times 18755249 (67.24%) aligned exactly 1 time 3802234 (13.63%) aligned >1 times 80.87% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 11080007 / 22557483 = 0.4912 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, 30 Jun 2020 01:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.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, 30 Jun 2020 01:31:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:31:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:31:11: 1000000 INFO @ Tue, 30 Jun 2020 01:31:17: 2000000 INFO @ Tue, 30 Jun 2020 01:31:24: 3000000 INFO @ Tue, 30 Jun 2020 01:31:30: 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, 30 Jun 2020 01:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.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, 30 Jun 2020 01:31:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:31:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:31:37: 5000000 INFO @ Tue, 30 Jun 2020 01:31:41: 1000000 INFO @ Tue, 30 Jun 2020 01:31:44: 6000000 INFO @ Tue, 30 Jun 2020 01:31:48: 2000000 INFO @ Tue, 30 Jun 2020 01:31:51: 7000000 INFO @ Tue, 30 Jun 2020 01:31:56: 3000000 INFO @ Tue, 30 Jun 2020 01:31:58: 8000000 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, 30 Jun 2020 01:32:03: 4000000 INFO @ Tue, 30 Jun 2020 01:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.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, 30 Jun 2020 01:32:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:32:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:32:05: 9000000 INFO @ Tue, 30 Jun 2020 01:32:10: 5000000 INFO @ Tue, 30 Jun 2020 01:32:11: 1000000 INFO @ Tue, 30 Jun 2020 01:32:12: 10000000 INFO @ Tue, 30 Jun 2020 01:32:17: 6000000 INFO @ Tue, 30 Jun 2020 01:32:18: 2000000 INFO @ Tue, 30 Jun 2020 01:32:19: 11000000 INFO @ Tue, 30 Jun 2020 01:32:23: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:32:23: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:32:23: #1 total tags in treatment: 11477476 INFO @ Tue, 30 Jun 2020 01:32:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:32:23: #1 tags after filtering in treatment: 11477476 INFO @ Tue, 30 Jun 2020 01:32:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:23: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:32:24: #2 number of paired peaks: 464 WARNING @ Tue, 30 Jun 2020 01:32:24: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:24: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:24: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:24: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:24: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:24: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 01:32:24: #2 alternative fragment length(s) may be 1,31,571 bps INFO @ Tue, 30 Jun 2020 01:32:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.05_model.r WARNING @ Tue, 30 Jun 2020 01:32:24: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:32:24: #2 You may need to consider one of the other alternative d(s): 1,31,571 WARNING @ Tue, 30 Jun 2020 01:32:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:32:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:24: 7000000 INFO @ Tue, 30 Jun 2020 01:32:26: 3000000 INFO @ Tue, 30 Jun 2020 01:32:32: 8000000 INFO @ Tue, 30 Jun 2020 01:32:33: 4000000 INFO @ Tue, 30 Jun 2020 01:32:39: 9000000 INFO @ Tue, 30 Jun 2020 01:32:40: 5000000 INFO @ Tue, 30 Jun 2020 01:32:46: 10000000 INFO @ Tue, 30 Jun 2020 01:32:47: 6000000 INFO @ Tue, 30 Jun 2020 01:32:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:53: 11000000 INFO @ Tue, 30 Jun 2020 01:32:54: 7000000 INFO @ Tue, 30 Jun 2020 01:32:56: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:32:56: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:32:56: #1 total tags in treatment: 11477476 INFO @ Tue, 30 Jun 2020 01:32:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:32:56: #1 tags after filtering in treatment: 11477476 INFO @ Tue, 30 Jun 2020 01:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:56: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:32:57: #2 number of paired peaks: 464 WARNING @ Tue, 30 Jun 2020 01:32:57: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:57: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:57: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:57: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:57: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:57: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 01:32:57: #2 alternative fragment length(s) may be 1,31,571 bps INFO @ Tue, 30 Jun 2020 01:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.10_model.r WARNING @ Tue, 30 Jun 2020 01:32:57: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:32:57: #2 You may need to consider one of the other alternative d(s): 1,31,571 WARNING @ Tue, 30 Jun 2020 01:32:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:32:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.05_summits.bed INFO @ Tue, 30 Jun 2020 01:32:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (830 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:33:01: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:33:08: 9000000 INFO @ Tue, 30 Jun 2020 01:33:14: 10000000 INFO @ Tue, 30 Jun 2020 01:33:21: 11000000 INFO @ Tue, 30 Jun 2020 01:33:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:33:24: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:33:24: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:33:24: #1 total tags in treatment: 11477476 INFO @ Tue, 30 Jun 2020 01:33:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:33:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:33:24: #1 tags after filtering in treatment: 11477476 INFO @ Tue, 30 Jun 2020 01:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:33:24: #1 finished! INFO @ Tue, 30 Jun 2020 01:33:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:33:25: #2 number of paired peaks: 464 WARNING @ Tue, 30 Jun 2020 01:33:25: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 30 Jun 2020 01:33:25: start model_add_line... INFO @ Tue, 30 Jun 2020 01:33:25: start X-correlation... INFO @ Tue, 30 Jun 2020 01:33:25: end of X-cor INFO @ Tue, 30 Jun 2020 01:33:25: #2 finished! INFO @ Tue, 30 Jun 2020 01:33:25: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 01:33:25: #2 alternative fragment length(s) may be 1,31,571 bps INFO @ Tue, 30 Jun 2020 01:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.20_model.r WARNING @ Tue, 30 Jun 2020 01:33:25: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:33:25: #2 You may need to consider one of the other alternative d(s): 1,31,571 WARNING @ Tue, 30 Jun 2020 01:33:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:33:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:33:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.10_summits.bed INFO @ Tue, 30 Jun 2020 01:33:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (476 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:33:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709763/SRX5709763.20_summits.bed INFO @ Tue, 30 Jun 2020 01:34:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 2 millis CompletedMACS2peakCalling