Job ID = 16435596 SRX = SRX13110378 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:52:31 prefetch.2.10.7: 1) Downloading 'SRR16918048'... 2022-08-02T01:52:31 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:53:04 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:53:05 prefetch.2.10.7: 'SRR16918048' is valid 2022-08-02T01:53:05 prefetch.2.10.7: 1) 'SRR16918048' was downloaded successfully 2022-08-02T01:53:05 prefetch.2.10.7: 'SRR16918048' has 0 unresolved dependencies Read 19626111 spots for SRR16918048/SRR16918048.sra Written 19626111 spots for SRR16918048/SRR16918048.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436195 ("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: 00:07:03 19626111 reads; of these: 19626111 (100.00%) were unpaired; of these: 721560 (3.68%) aligned 0 times 15935708 (81.20%) aligned exactly 1 time 2968843 (15.13%) aligned >1 times 96.32% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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 8 files... [bam_rmdupse_core] 2041679 / 18904551 = 0.1080 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 11:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.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 11:06:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:10: 1000000 INFO @ Tue, 02 Aug 2022 11:06:18: 2000000 INFO @ Tue, 02 Aug 2022 11:06:25: 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 11:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.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 11:06:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:33: 4000000 INFO @ Tue, 02 Aug 2022 11:06:38: 1000000 INFO @ Tue, 02 Aug 2022 11:06:40: 5000000 INFO @ Tue, 02 Aug 2022 11:06:46: 2000000 INFO @ Tue, 02 Aug 2022 11:06:47: 6000000 INFO @ Tue, 02 Aug 2022 11:06:53: 3000000 INFO @ Tue, 02 Aug 2022 11:06:54: 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 11:07:00: 4000000 INFO @ Tue, 02 Aug 2022 11:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.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 11:07:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:07:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:07:01: 8000000 INFO @ Tue, 02 Aug 2022 11:07:08: 5000000 INFO @ Tue, 02 Aug 2022 11:07:09: 9000000 INFO @ Tue, 02 Aug 2022 11:07:10: 1000000 INFO @ Tue, 02 Aug 2022 11:07:16: 6000000 INFO @ Tue, 02 Aug 2022 11:07:17: 10000000 INFO @ Tue, 02 Aug 2022 11:07:18: 2000000 INFO @ Tue, 02 Aug 2022 11:07:23: 7000000 INFO @ Tue, 02 Aug 2022 11:07:24: 11000000 INFO @ Tue, 02 Aug 2022 11:07:26: 3000000 INFO @ Tue, 02 Aug 2022 11:07:31: 8000000 INFO @ Tue, 02 Aug 2022 11:07:32: 12000000 INFO @ Tue, 02 Aug 2022 11:07:34: 4000000 INFO @ Tue, 02 Aug 2022 11:07:38: 9000000 INFO @ Tue, 02 Aug 2022 11:07:39: 13000000 INFO @ Tue, 02 Aug 2022 11:07:41: 5000000 INFO @ Tue, 02 Aug 2022 11:07:46: 10000000 INFO @ Tue, 02 Aug 2022 11:07:46: 14000000 INFO @ Tue, 02 Aug 2022 11:07:49: 6000000 INFO @ Tue, 02 Aug 2022 11:07:54: 11000000 INFO @ Tue, 02 Aug 2022 11:07:54: 15000000 INFO @ Tue, 02 Aug 2022 11:07:57: 7000000 INFO @ Tue, 02 Aug 2022 11:08:01: 12000000 INFO @ Tue, 02 Aug 2022 11:08:01: 16000000 INFO @ Tue, 02 Aug 2022 11:08:04: 8000000 INFO @ Tue, 02 Aug 2022 11:08:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:08:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:08:07: #1 total tags in treatment: 16862872 INFO @ Tue, 02 Aug 2022 11:08:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:08:07: #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 11:08:08: #1 tags after filtering in treatment: 16862872 INFO @ Tue, 02 Aug 2022 11:08:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:08:08: #1 finished! INFO @ Tue, 02 Aug 2022 11:08:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:08:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:08:08: 13000000 INFO @ Tue, 02 Aug 2022 11:08:09: #2 number of paired peaks: 204 WARNING @ Tue, 02 Aug 2022 11:08:09: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 02 Aug 2022 11:08:09: start model_add_line... INFO @ Tue, 02 Aug 2022 11:08:09: start X-correlation... INFO @ Tue, 02 Aug 2022 11:08:09: end of X-cor INFO @ Tue, 02 Aug 2022 11:08:09: #2 finished! INFO @ Tue, 02 Aug 2022 11:08:09: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 11:08:09: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 02 Aug 2022 11:08:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.05_model.r WARNING @ Tue, 02 Aug 2022 11:08:09: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:08:09: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 02 Aug 2022 11:08:09: #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 11:08:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:08:12: 9000000 INFO @ Tue, 02 Aug 2022 11:08:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:08:19: 10000000 INFO @ Tue, 02 Aug 2022 11:08:22: 15000000 INFO @ Tue, 02 Aug 2022 11:08:26: 11000000 INFO @ Tue, 02 Aug 2022 11:08:29: 16000000 INFO @ Tue, 02 Aug 2022 11:08:33: 12000000 INFO @ Tue, 02 Aug 2022 11:08:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:08:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:08:36: #1 total tags in treatment: 16862872 INFO @ Tue, 02 Aug 2022 11:08:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:08:36: #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 11:08:36: #1 tags after filtering in treatment: 16862872 INFO @ Tue, 02 Aug 2022 11:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:08:36: #1 finished! INFO @ Tue, 02 Aug 2022 11:08:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:08:37: #2 number of paired peaks: 204 WARNING @ Tue, 02 Aug 2022 11:08:37: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 02 Aug 2022 11:08:37: start model_add_line... INFO @ Tue, 02 Aug 2022 11:08:37: start X-correlation... INFO @ Tue, 02 Aug 2022 11:08:37: end of X-cor INFO @ Tue, 02 Aug 2022 11:08:37: #2 finished! INFO @ Tue, 02 Aug 2022 11:08:37: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 11:08:37: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 02 Aug 2022 11:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.10_model.r WARNING @ Tue, 02 Aug 2022 11:08:37: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:08:37: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 02 Aug 2022 11:08:37: #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 11:08:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:08:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:08:39: 13000000 INFO @ Tue, 02 Aug 2022 11:08:45: 14000000 INFO @ Tue, 02 Aug 2022 11:08:51: 15000000 INFO @ Tue, 02 Aug 2022 11:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.05_summits.bed INFO @ Tue, 02 Aug 2022 11:08:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:08:57: 16000000 INFO @ Tue, 02 Aug 2022 11:09:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:09:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:09:02: #1 total tags in treatment: 16862872 INFO @ Tue, 02 Aug 2022 11:09:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:09:02: #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 11:09:02: #1 tags after filtering in treatment: 16862872 INFO @ Tue, 02 Aug 2022 11:09:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:09:02: #1 finished! INFO @ Tue, 02 Aug 2022 11:09:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:09:03: #2 number of paired peaks: 204 WARNING @ Tue, 02 Aug 2022 11:09:03: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 02 Aug 2022 11:09:03: start model_add_line... INFO @ Tue, 02 Aug 2022 11:09:04: start X-correlation... INFO @ Tue, 02 Aug 2022 11:09:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:09:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:09:04: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 11:09:04: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 02 Aug 2022 11:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.20_model.r WARNING @ Tue, 02 Aug 2022 11:09:04: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:09:04: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 02 Aug 2022 11:09:04: #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 11:09:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:09:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.10_summits.bed INFO @ Tue, 02 Aug 2022 11:09:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (432 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:09:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110378/SRX13110378.20_summits.bed INFO @ Tue, 02 Aug 2022 11:09:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 14 millis CompletedMACS2peakCalling