Job ID = 16435582 SRX = SRX13110361 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:47:31 prefetch.2.10.7: 1) Downloading 'SRR16918031'... 2022-08-02T01:47:31 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:48:13 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:48:14 prefetch.2.10.7: 'SRR16918031' is valid 2022-08-02T01:48:14 prefetch.2.10.7: 1) 'SRR16918031' was downloaded successfully 2022-08-02T01:48:14 prefetch.2.10.7: 'SRR16918031' has 0 unresolved dependencies Read 20865377 spots for SRR16918031/SRR16918031.sra Written 20865377 spots for SRR16918031/SRR16918031.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436152 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:04 20865377 reads; of these: 20865377 (100.00%) were unpaired; of these: 1857634 (8.90%) aligned 0 times 16038328 (76.87%) aligned exactly 1 time 2969415 (14.23%) aligned >1 times 91.10% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 2163387 / 19007743 = 0.1138 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 10:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.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 10:59:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:59:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:59:50: 1000000 INFO @ Tue, 02 Aug 2022 10:59:56: 2000000 INFO @ Tue, 02 Aug 2022 11:00:02: 3000000 INFO @ Tue, 02 Aug 2022 11:00:08: 4000000 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 11:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.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 11:00:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:14: 5000000 INFO @ Tue, 02 Aug 2022 11:00:22: 6000000 INFO @ Tue, 02 Aug 2022 11:00:22: 1000000 INFO @ Tue, 02 Aug 2022 11:00:30: 7000000 INFO @ Tue, 02 Aug 2022 11:00:31: 2000000 INFO @ Tue, 02 Aug 2022 11:00:38: 8000000 INFO @ Tue, 02 Aug 2022 11:00:39: 3000000 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 11:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.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 11:00:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:46: 9000000 INFO @ Tue, 02 Aug 2022 11:00:48: 4000000 INFO @ Tue, 02 Aug 2022 11:00:52: 1000000 INFO @ Tue, 02 Aug 2022 11:00:53: 10000000 INFO @ Tue, 02 Aug 2022 11:00:57: 5000000 INFO @ Tue, 02 Aug 2022 11:01:01: 2000000 INFO @ Tue, 02 Aug 2022 11:01:01: 11000000 INFO @ Tue, 02 Aug 2022 11:01:06: 6000000 INFO @ Tue, 02 Aug 2022 11:01:09: 12000000 INFO @ Tue, 02 Aug 2022 11:01:10: 3000000 INFO @ Tue, 02 Aug 2022 11:01:15: 7000000 INFO @ Tue, 02 Aug 2022 11:01:17: 13000000 INFO @ Tue, 02 Aug 2022 11:01:19: 4000000 INFO @ Tue, 02 Aug 2022 11:01:23: 8000000 INFO @ Tue, 02 Aug 2022 11:01:25: 14000000 INFO @ Tue, 02 Aug 2022 11:01:28: 5000000 INFO @ Tue, 02 Aug 2022 11:01:32: 9000000 INFO @ Tue, 02 Aug 2022 11:01:33: 15000000 INFO @ Tue, 02 Aug 2022 11:01:37: 6000000 INFO @ Tue, 02 Aug 2022 11:01:41: 10000000 INFO @ Tue, 02 Aug 2022 11:01:41: 16000000 INFO @ Tue, 02 Aug 2022 11:01:45: 7000000 INFO @ Tue, 02 Aug 2022 11:01:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:47: #1 total tags in treatment: 16844356 INFO @ Tue, 02 Aug 2022 11:01:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:47: #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 11:01:48: #1 tags after filtering in treatment: 16844356 INFO @ Tue, 02 Aug 2022 11:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:48: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:49: #2 number of paired peaks: 209 WARNING @ Tue, 02 Aug 2022 11:01:49: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 02 Aug 2022 11:01:49: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:49: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:49: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:49: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:49: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:01:49: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 11:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.05_model.r WARNING @ Tue, 02 Aug 2022 11:01:49: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:01:49: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 11:01:49: #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 11:01:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:49: 11000000 INFO @ Tue, 02 Aug 2022 11:01:54: 8000000 INFO @ Tue, 02 Aug 2022 11:01:58: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:02:02: 9000000 INFO @ Tue, 02 Aug 2022 11:02:06: 13000000 INFO @ Tue, 02 Aug 2022 11:02:10: 10000000 INFO @ Tue, 02 Aug 2022 11:02:15: 14000000 INFO @ Tue, 02 Aug 2022 11:02:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:02:19: 11000000 INFO @ Tue, 02 Aug 2022 11:02:23: 15000000 INFO @ Tue, 02 Aug 2022 11:02:27: 12000000 INFO @ Tue, 02 Aug 2022 11:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:02:32: 16000000 INFO @ Tue, 02 Aug 2022 11:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.05_summits.bed INFO @ Tue, 02 Aug 2022 11:02:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (804 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:02:35: 13000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:02:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:02:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:02:39: #1 total tags in treatment: 16844356 INFO @ Tue, 02 Aug 2022 11:02:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:02:39: #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 11:02:39: #1 tags after filtering in treatment: 16844356 INFO @ Tue, 02 Aug 2022 11:02:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:02:39: #1 finished! INFO @ Tue, 02 Aug 2022 11:02:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:02:40: #2 number of paired peaks: 209 WARNING @ Tue, 02 Aug 2022 11:02:40: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 02 Aug 2022 11:02:40: start model_add_line... INFO @ Tue, 02 Aug 2022 11:02:40: start X-correlation... INFO @ Tue, 02 Aug 2022 11:02:40: end of X-cor INFO @ Tue, 02 Aug 2022 11:02:40: #2 finished! INFO @ Tue, 02 Aug 2022 11:02:40: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:02:40: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 11:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.10_model.r WARNING @ Tue, 02 Aug 2022 11:02:41: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:02:41: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 11:02:41: #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 11:02:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:02:43: 14000000 INFO @ Tue, 02 Aug 2022 11:02:51: 15000000 INFO @ Tue, 02 Aug 2022 11:02:59: 16000000 INFO @ Tue, 02 Aug 2022 11:03:05: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:03:05: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:03:05: #1 total tags in treatment: 16844356 INFO @ Tue, 02 Aug 2022 11:03:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:03:05: #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 11:03:05: #1 tags after filtering in treatment: 16844356 INFO @ Tue, 02 Aug 2022 11:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:03:05: #1 finished! INFO @ Tue, 02 Aug 2022 11:03:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:03:06: #2 number of paired peaks: 209 WARNING @ Tue, 02 Aug 2022 11:03:06: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 02 Aug 2022 11:03:06: start model_add_line... INFO @ Tue, 02 Aug 2022 11:03:06: start X-correlation... INFO @ Tue, 02 Aug 2022 11:03:06: end of X-cor INFO @ Tue, 02 Aug 2022 11:03:06: #2 finished! INFO @ Tue, 02 Aug 2022 11:03:06: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:03:06: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 11:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.20_model.r WARNING @ Tue, 02 Aug 2022 11:03:06: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:03:06: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 11:03:06: #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 11:03:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:03:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.10_summits.bed INFO @ Tue, 02 Aug 2022 11:03:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (450 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:03:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:03:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:03:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:03:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110361/SRX13110361.20_summits.bed INFO @ Tue, 02 Aug 2022 11:03:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 27 millis CompletedMACS2peakCalling