Job ID = 16435538 SRX = SRX13110350 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:46:48 prefetch.2.10.7: 1) Downloading 'SRR16918020'... 2022-08-02T01:46:49 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:46:57 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:46:58 prefetch.2.10.7: 'SRR16918020' is valid 2022-08-02T01:46:58 prefetch.2.10.7: 1) 'SRR16918020' was downloaded successfully 2022-08-02T01:46:58 prefetch.2.10.7: 'SRR16918020' has 0 unresolved dependencies Read 15997017 spots for SRR16918020/SRR16918020.sra Written 15997017 spots for SRR16918020/SRR16918020.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436148 ("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: 00:06:24 15997017 reads; of these: 15997017 (100.00%) were unpaired; of these: 1176920 (7.36%) aligned 0 times 12236083 (76.49%) aligned exactly 1 time 2584014 (16.15%) aligned >1 times 92.64% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 1899583 / 14820097 = 0.1282 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 11:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.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 11:00:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:50: 1000000 INFO @ Tue, 02 Aug 2022 11:00:58: 2000000 INFO @ Tue, 02 Aug 2022 11:01:05: 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 11:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.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 11:01:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:13: 4000000 INFO @ Tue, 02 Aug 2022 11:01:20: 1000000 INFO @ Tue, 02 Aug 2022 11:01:21: 5000000 INFO @ Tue, 02 Aug 2022 11:01:29: 6000000 INFO @ Tue, 02 Aug 2022 11:01:31: 2000000 INFO @ Tue, 02 Aug 2022 11:01:38: 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 11:01:41: 3000000 INFO @ Tue, 02 Aug 2022 11:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.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 11:01:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:47: 8000000 INFO @ Tue, 02 Aug 2022 11:01:50: 4000000 INFO @ Tue, 02 Aug 2022 11:01:51: 1000000 INFO @ Tue, 02 Aug 2022 11:01:56: 9000000 INFO @ Tue, 02 Aug 2022 11:02:00: 5000000 INFO @ Tue, 02 Aug 2022 11:02:00: 2000000 INFO @ Tue, 02 Aug 2022 11:02:04: 10000000 INFO @ Tue, 02 Aug 2022 11:02:09: 6000000 INFO @ Tue, 02 Aug 2022 11:02:10: 3000000 INFO @ Tue, 02 Aug 2022 11:02:13: 11000000 INFO @ Tue, 02 Aug 2022 11:02:20: 7000000 INFO @ Tue, 02 Aug 2022 11:02:20: 4000000 INFO @ Tue, 02 Aug 2022 11:02:21: 12000000 INFO @ Tue, 02 Aug 2022 11:02:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:02:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:02:30: #1 total tags in treatment: 12920514 INFO @ Tue, 02 Aug 2022 11:02:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:02:30: #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 11:02:30: #1 tags after filtering in treatment: 12920514 INFO @ Tue, 02 Aug 2022 11:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:02:30: #1 finished! INFO @ Tue, 02 Aug 2022 11:02:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:02:30: 5000000 INFO @ Tue, 02 Aug 2022 11:02:30: 8000000 INFO @ Tue, 02 Aug 2022 11:02:31: #2 number of paired peaks: 444 WARNING @ Tue, 02 Aug 2022 11:02:31: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Tue, 02 Aug 2022 11:02:31: start model_add_line... INFO @ Tue, 02 Aug 2022 11:02:31: start X-correlation... INFO @ Tue, 02 Aug 2022 11:02:31: end of X-cor INFO @ Tue, 02 Aug 2022 11:02:31: #2 finished! INFO @ Tue, 02 Aug 2022 11:02:31: #2 predicted fragment length is 149 bps INFO @ Tue, 02 Aug 2022 11:02:31: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 02 Aug 2022 11:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.05_model.r WARNING @ Tue, 02 Aug 2022 11:02:31: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:02:31: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Tue, 02 Aug 2022 11:02:31: #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 11:02:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:02:40: 9000000 INFO @ Tue, 02 Aug 2022 11:02:40: 6000000 INFO @ Tue, 02 Aug 2022 11:02:50: 7000000 INFO @ Tue, 02 Aug 2022 11:02:50: 10000000 INFO @ Tue, 02 Aug 2022 11:03:00: 8000000 INFO @ Tue, 02 Aug 2022 11:03:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:03:00: 11000000 INFO @ Tue, 02 Aug 2022 11:03:08: 9000000 INFO @ Tue, 02 Aug 2022 11:03:09: 12000000 INFO @ Tue, 02 Aug 2022 11:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.05_summits.bed INFO @ Tue, 02 Aug 2022 11:03:14: Done! pass1 - making usageList (7 chroms): 13 millis pass2 - checking and writing primary data (5655 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:03:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:03:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:03:18: #1 total tags in treatment: 12920514 INFO @ Tue, 02 Aug 2022 11:03:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:03:18: #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 11:03:18: 10000000 INFO @ Tue, 02 Aug 2022 11:03:18: #1 tags after filtering in treatment: 12920514 INFO @ Tue, 02 Aug 2022 11:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:03:18: #1 finished! INFO @ Tue, 02 Aug 2022 11:03:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:03:19: #2 number of paired peaks: 444 WARNING @ Tue, 02 Aug 2022 11:03:19: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Tue, 02 Aug 2022 11:03:19: start model_add_line... INFO @ Tue, 02 Aug 2022 11:03:19: start X-correlation... INFO @ Tue, 02 Aug 2022 11:03:19: end of X-cor INFO @ Tue, 02 Aug 2022 11:03:19: #2 finished! INFO @ Tue, 02 Aug 2022 11:03:19: #2 predicted fragment length is 149 bps INFO @ Tue, 02 Aug 2022 11:03:19: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 02 Aug 2022 11:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.10_model.r WARNING @ Tue, 02 Aug 2022 11:03:20: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:03:20: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Tue, 02 Aug 2022 11:03:20: #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 11:03:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:03:27: 11000000 INFO @ Tue, 02 Aug 2022 11:03:36: 12000000 INFO @ Tue, 02 Aug 2022 11:03:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:03:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:03:44: #1 total tags in treatment: 12920514 INFO @ Tue, 02 Aug 2022 11:03:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:03:44: #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 11:03:44: #1 tags after filtering in treatment: 12920514 INFO @ Tue, 02 Aug 2022 11:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:03:44: #1 finished! INFO @ Tue, 02 Aug 2022 11:03:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:03:45: #2 number of paired peaks: 444 WARNING @ Tue, 02 Aug 2022 11:03:45: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Tue, 02 Aug 2022 11:03:45: start model_add_line... INFO @ Tue, 02 Aug 2022 11:03:45: start X-correlation... INFO @ Tue, 02 Aug 2022 11:03:45: end of X-cor INFO @ Tue, 02 Aug 2022 11:03:45: #2 finished! INFO @ Tue, 02 Aug 2022 11:03:45: #2 predicted fragment length is 149 bps INFO @ Tue, 02 Aug 2022 11:03:45: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 02 Aug 2022 11:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.20_model.r WARNING @ Tue, 02 Aug 2022 11:03:45: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:03:45: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Tue, 02 Aug 2022 11:03:45: #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 11:03:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:03:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:04:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:04:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.10_summits.bed INFO @ Tue, 02 Aug 2022 11:04:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2948 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:04:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110350/SRX13110350.20_summits.bed INFO @ Tue, 02 Aug 2022 11:04:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。