Job ID = 16434829 SRX = SRX10435504 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28415103 spots for SRR14060920/SRR14060920.sra Written 28415103 spots for SRR14060920/SRR14060920.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434891 ("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: 00:08:37 28415103 reads; of these: 28415103 (100.00%) were unpaired; of these: 4747788 (16.71%) aligned 0 times 20184839 (71.04%) aligned exactly 1 time 3482476 (12.26%) aligned >1 times 83.29% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 6292981 / 23667315 = 0.2659 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 10:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.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 10:12:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:11: 1000000 INFO @ Tue, 02 Aug 2022 10:12:19: 2000000 INFO @ Tue, 02 Aug 2022 10:12:25: 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 10:12:32: 4000000 INFO @ Tue, 02 Aug 2022 10:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.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 10:12:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:39: 5000000 INFO @ Tue, 02 Aug 2022 10:12:41: 1000000 INFO @ Tue, 02 Aug 2022 10:12:47: 6000000 INFO @ Tue, 02 Aug 2022 10:12:48: 2000000 INFO @ Tue, 02 Aug 2022 10:12:53: 7000000 INFO @ Tue, 02 Aug 2022 10:12:55: 3000000 INFO @ Tue, 02 Aug 2022 10:13:00: 8000000 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 10:13:02: 4000000 INFO @ Tue, 02 Aug 2022 10:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.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 10:13:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:13:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:13:07: 9000000 INFO @ Tue, 02 Aug 2022 10:13:10: 5000000 INFO @ Tue, 02 Aug 2022 10:13:12: 1000000 INFO @ Tue, 02 Aug 2022 10:13:14: 10000000 INFO @ Tue, 02 Aug 2022 10:13:17: 6000000 INFO @ Tue, 02 Aug 2022 10:13:21: 2000000 INFO @ Tue, 02 Aug 2022 10:13:21: 11000000 INFO @ Tue, 02 Aug 2022 10:13:25: 7000000 INFO @ Tue, 02 Aug 2022 10:13:29: 12000000 INFO @ Tue, 02 Aug 2022 10:13:29: 3000000 INFO @ Tue, 02 Aug 2022 10:13:33: 8000000 INFO @ Tue, 02 Aug 2022 10:13:36: 13000000 INFO @ Tue, 02 Aug 2022 10:13:37: 4000000 INFO @ Tue, 02 Aug 2022 10:13:41: 9000000 INFO @ Tue, 02 Aug 2022 10:13:44: 14000000 INFO @ Tue, 02 Aug 2022 10:13:45: 5000000 INFO @ Tue, 02 Aug 2022 10:13:48: 10000000 INFO @ Tue, 02 Aug 2022 10:13:51: 15000000 INFO @ Tue, 02 Aug 2022 10:13:52: 6000000 INFO @ Tue, 02 Aug 2022 10:13:56: 11000000 INFO @ Tue, 02 Aug 2022 10:13:58: 16000000 INFO @ Tue, 02 Aug 2022 10:14:00: 7000000 INFO @ Tue, 02 Aug 2022 10:14:03: 12000000 INFO @ Tue, 02 Aug 2022 10:14:06: 17000000 INFO @ Tue, 02 Aug 2022 10:14:07: 8000000 INFO @ Tue, 02 Aug 2022 10:14:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:14:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:14:09: #1 total tags in treatment: 17374334 INFO @ Tue, 02 Aug 2022 10:14:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:14:09: #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 10:14:09: #1 tags after filtering in treatment: 17374334 INFO @ Tue, 02 Aug 2022 10:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:14:09: #1 finished! INFO @ Tue, 02 Aug 2022 10:14:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:14:10: #2 number of paired peaks: 291 WARNING @ Tue, 02 Aug 2022 10:14:10: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 02 Aug 2022 10:14:10: start model_add_line... INFO @ Tue, 02 Aug 2022 10:14:10: start X-correlation... INFO @ Tue, 02 Aug 2022 10:14:10: end of X-cor INFO @ Tue, 02 Aug 2022 10:14:10: #2 finished! INFO @ Tue, 02 Aug 2022 10:14:10: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 10:14:10: #2 alternative fragment length(s) may be 4,133 bps INFO @ Tue, 02 Aug 2022 10:14:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.05_model.r WARNING @ Tue, 02 Aug 2022 10:14:10: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:14:10: #2 You may need to consider one of the other alternative d(s): 4,133 WARNING @ Tue, 02 Aug 2022 10:14:10: #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 10:14:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:14:11: 13000000 INFO @ Tue, 02 Aug 2022 10:14:15: 9000000 INFO @ Tue, 02 Aug 2022 10:14:18: 14000000 INFO @ Tue, 02 Aug 2022 10:14:22: 10000000 INFO @ Tue, 02 Aug 2022 10:14:25: 15000000 INFO @ Tue, 02 Aug 2022 10:14:29: 11000000 INFO @ Tue, 02 Aug 2022 10:14:32: 16000000 INFO @ Tue, 02 Aug 2022 10:14:35: 12000000 INFO @ Tue, 02 Aug 2022 10:14:39: 17000000 INFO @ Tue, 02 Aug 2022 10:14:42: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:14:42: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:14:42: #1 total tags in treatment: 17374334 INFO @ Tue, 02 Aug 2022 10:14:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:14:42: #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 10:14:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:14:42: 13000000 INFO @ Tue, 02 Aug 2022 10:14:42: #1 tags after filtering in treatment: 17374334 INFO @ Tue, 02 Aug 2022 10:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:14:42: #1 finished! INFO @ Tue, 02 Aug 2022 10:14:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:14:43: #2 number of paired peaks: 291 WARNING @ Tue, 02 Aug 2022 10:14:43: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 02 Aug 2022 10:14:43: start model_add_line... INFO @ Tue, 02 Aug 2022 10:14:44: start X-correlation... INFO @ Tue, 02 Aug 2022 10:14:44: end of X-cor INFO @ Tue, 02 Aug 2022 10:14:44: #2 finished! INFO @ Tue, 02 Aug 2022 10:14:44: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 10:14:44: #2 alternative fragment length(s) may be 4,133 bps INFO @ Tue, 02 Aug 2022 10:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.10_model.r WARNING @ Tue, 02 Aug 2022 10:14:44: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:14:44: #2 You may need to consider one of the other alternative d(s): 4,133 WARNING @ Tue, 02 Aug 2022 10:14:44: #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 10:14:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:14:49: 14000000 INFO @ Tue, 02 Aug 2022 10:14:56: 15000000 INFO @ Tue, 02 Aug 2022 10:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.05_summits.bed INFO @ Tue, 02 Aug 2022 10:14:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2410 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:02: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:15:09: 17000000 INFO @ Tue, 02 Aug 2022 10:15:12: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:15:12: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:15:12: #1 total tags in treatment: 17374334 INFO @ Tue, 02 Aug 2022 10:15:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:12: #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 10:15:12: #1 tags after filtering in treatment: 17374334 INFO @ Tue, 02 Aug 2022 10:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:12: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:13: #2 number of paired peaks: 291 WARNING @ Tue, 02 Aug 2022 10:15:13: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:13: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:13: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:13: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:13: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:13: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 10:15:13: #2 alternative fragment length(s) may be 4,133 bps INFO @ Tue, 02 Aug 2022 10:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.20_model.r WARNING @ Tue, 02 Aug 2022 10:15:13: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:13: #2 You may need to consider one of the other alternative d(s): 4,133 WARNING @ Tue, 02 Aug 2022 10:15:13: #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 10:15:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.10_summits.bed INFO @ Tue, 02 Aug 2022 10:15:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435504/SRX10435504.20_summits.bed INFO @ Tue, 02 Aug 2022 10:16:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (837 records, 4 fields): 37 millis CompletedMACS2peakCalling