Job ID = 16433521 SRX = SRX10925652 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20482968 spots for SRR14580042/SRR14580042.sra Written 20482968 spots for SRR14580042/SRR14580042.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434631 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:04 20482968 reads; of these: 20482968 (100.00%) were unpaired; of these: 7076598 (34.55%) aligned 0 times 10875389 (53.09%) aligned exactly 1 time 2530981 (12.36%) aligned >1 times 65.45% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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 8 files... [bam_rmdupse_core] 2062435 / 13406370 = 0.1538 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.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, 02 Aug 2022 09:54:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:01: 1000000 INFO @ Tue, 02 Aug 2022 09:55:10: 2000000 INFO @ Tue, 02 Aug 2022 09:55:17: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:55:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.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, 02 Aug 2022 09:55:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:24: 4000000 INFO @ Tue, 02 Aug 2022 09:55:32: 5000000 INFO @ Tue, 02 Aug 2022 09:55:34: 1000000 INFO @ Tue, 02 Aug 2022 09:55:41: 6000000 INFO @ Tue, 02 Aug 2022 09:55:43: 2000000 INFO @ Tue, 02 Aug 2022 09:55:49: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:55:53: 3000000 INFO @ Tue, 02 Aug 2022 09:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.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, 02 Aug 2022 09:55:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:58: 8000000 INFO @ Tue, 02 Aug 2022 09:56:03: 4000000 INFO @ Tue, 02 Aug 2022 09:56:04: 1000000 INFO @ Tue, 02 Aug 2022 09:56:08: 9000000 INFO @ Tue, 02 Aug 2022 09:56:13: 2000000 INFO @ Tue, 02 Aug 2022 09:56:13: 5000000 INFO @ Tue, 02 Aug 2022 09:56:17: 10000000 INFO @ Tue, 02 Aug 2022 09:56:22: 3000000 INFO @ Tue, 02 Aug 2022 09:56:24: 6000000 INFO @ Tue, 02 Aug 2022 09:56:27: 11000000 INFO @ Tue, 02 Aug 2022 09:56:31: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:56:31: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:56:31: #1 total tags in treatment: 11343935 INFO @ Tue, 02 Aug 2022 09:56:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:56:31: #1 tags after filtering in treatment: 11343935 INFO @ Tue, 02 Aug 2022 09:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:31: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:32: #2 number of paired peaks: 270 WARNING @ Tue, 02 Aug 2022 09:56:32: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:32: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:32: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:33: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:33: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:33: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:56:33: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 02 Aug 2022 09:56:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.05_model.r WARNING @ Tue, 02 Aug 2022 09:56:33: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:56:33: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 02 Aug 2022 09:56:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:56:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:56:33: 4000000 INFO @ Tue, 02 Aug 2022 09:56:33: 7000000 INFO @ Tue, 02 Aug 2022 09:56:42: 5000000 INFO @ Tue, 02 Aug 2022 09:56:42: 8000000 INFO @ Tue, 02 Aug 2022 09:56:52: 6000000 INFO @ Tue, 02 Aug 2022 09:56:52: 9000000 INFO @ Tue, 02 Aug 2022 09:56:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:00: 7000000 INFO @ Tue, 02 Aug 2022 09:57:01: 10000000 INFO @ Tue, 02 Aug 2022 09:57:07: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:57:11: 11000000 INFO @ Tue, 02 Aug 2022 09:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.05_summits.bed INFO @ Tue, 02 Aug 2022 09:57:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1665 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:57:14: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:57:14: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:57:14: #1 total tags in treatment: 11343935 INFO @ Tue, 02 Aug 2022 09:57:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:57:15: #1 tags after filtering in treatment: 11343935 INFO @ Tue, 02 Aug 2022 09:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:15: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:57:15: 9000000 INFO @ Tue, 02 Aug 2022 09:57:16: #2 number of paired peaks: 270 WARNING @ Tue, 02 Aug 2022 09:57:16: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 02 Aug 2022 09:57:16: start model_add_line... INFO @ Tue, 02 Aug 2022 09:57:16: start X-correlation... INFO @ Tue, 02 Aug 2022 09:57:16: end of X-cor INFO @ Tue, 02 Aug 2022 09:57:16: #2 finished! INFO @ Tue, 02 Aug 2022 09:57:16: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:57:16: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 02 Aug 2022 09:57:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.10_model.r WARNING @ Tue, 02 Aug 2022 09:57:16: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:57:16: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 02 Aug 2022 09:57:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:57:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:57:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:57:22: 10000000 INFO @ Tue, 02 Aug 2022 09:57:30: 11000000 INFO @ Tue, 02 Aug 2022 09:57:33: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:57:33: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:57:33: #1 total tags in treatment: 11343935 INFO @ Tue, 02 Aug 2022 09:57:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:57:33: #1 tags after filtering in treatment: 11343935 INFO @ Tue, 02 Aug 2022 09:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:33: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:57:34: #2 number of paired peaks: 270 WARNING @ Tue, 02 Aug 2022 09:57:34: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 02 Aug 2022 09:57:34: start model_add_line... INFO @ Tue, 02 Aug 2022 09:57:35: start X-correlation... INFO @ Tue, 02 Aug 2022 09:57:35: end of X-cor INFO @ Tue, 02 Aug 2022 09:57:35: #2 finished! INFO @ Tue, 02 Aug 2022 09:57:35: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 09:57:35: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 02 Aug 2022 09:57:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.20_model.r WARNING @ Tue, 02 Aug 2022 09:57:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:57:35: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 02 Aug 2022 09:57:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:57:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:57:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:57:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.10_summits.bed INFO @ Tue, 02 Aug 2022 09:57:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:58:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925652/SRX10925652.20_summits.bed INFO @ Tue, 02 Aug 2022 09:58:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 14 millis CompletedMACS2peakCalling