Job ID = 16435584 SRX = SRX13110365 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:47:45 prefetch.2.10.7: 1) Downloading 'SRR16918035'... 2022-08-02T01:47:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:48:19 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:48:19 prefetch.2.10.7: 1) 'SRR16918035' was downloaded successfully 2022-08-02T01:48:19 prefetch.2.10.7: 'SRR16918035' has 0 unresolved dependencies Read 20894769 spots for SRR16918035/SRR16918035.sra Written 20894769 spots for SRR16918035/SRR16918035.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436144 ("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: 00:04:21 20894769 reads; of these: 20894769 (100.00%) were unpaired; of these: 14085868 (67.41%) aligned 0 times 5768437 (27.61%) aligned exactly 1 time 1040464 (4.98%) aligned >1 times 32.59% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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_rmdupse_core] 819576 / 6808901 = 0.1204 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 10:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.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 10:56:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:56:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:56:15: 1000000 INFO @ Tue, 02 Aug 2022 10:56:21: 2000000 INFO @ Tue, 02 Aug 2022 10:56:26: 3000000 INFO @ Tue, 02 Aug 2022 10:56:31: 4000000 INFO @ Tue, 02 Aug 2022 10:56:36: 5000000 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 10:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.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 10:56:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:56:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:56:41: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:56:41: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:56:41: #1 total tags in treatment: 5989325 INFO @ Tue, 02 Aug 2022 10:56:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:41: #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 10:56:41: #1 tags after filtering in treatment: 5989325 INFO @ Tue, 02 Aug 2022 10:56:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:56:41: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:41: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 10:56:41: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 10:56:41: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:41: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:41: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:41: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:41: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 10:56:41: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 02 Aug 2022 10:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.05_model.r WARNING @ Tue, 02 Aug 2022 10:56:41: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:56:41: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 02 Aug 2022 10:56:41: #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 10:56:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:46: 1000000 INFO @ Tue, 02 Aug 2022 10:56:52: 2000000 INFO @ Tue, 02 Aug 2022 10:56:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:58: 3000000 INFO @ Tue, 02 Aug 2022 10:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.05_summits.bed INFO @ Tue, 02 Aug 2022 10:57:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:57:04: 4000000 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 10:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.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 10:57:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:57:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:10: 5000000 INFO @ Tue, 02 Aug 2022 10:57:15: 1000000 INFO @ Tue, 02 Aug 2022 10:57:16: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:16: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:16: #1 total tags in treatment: 5989325 INFO @ Tue, 02 Aug 2022 10:57:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:16: #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 10:57:16: #1 tags after filtering in treatment: 5989325 INFO @ Tue, 02 Aug 2022 10:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:16: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:17: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 10:57:17: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 10:57:17: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:17: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:17: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:17: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:17: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 10:57:17: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 02 Aug 2022 10:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.10_model.r WARNING @ Tue, 02 Aug 2022 10:57:17: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:57:17: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 02 Aug 2022 10:57:17: #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 10:57:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:57:20: 2000000 INFO @ Tue, 02 Aug 2022 10:57:26: 3000000 INFO @ Tue, 02 Aug 2022 10:57:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:57:31: 4000000 INFO @ Tue, 02 Aug 2022 10:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.10_summits.bed INFO @ Tue, 02 Aug 2022 10:57:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:57:36: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:57:41: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:41: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:41: #1 total tags in treatment: 5989325 INFO @ Tue, 02 Aug 2022 10:57:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:41: #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 10:57:41: #1 tags after filtering in treatment: 5989325 INFO @ Tue, 02 Aug 2022 10:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:41: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:42: #2 number of paired peaks: 288 WARNING @ Tue, 02 Aug 2022 10:57:42: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 02 Aug 2022 10:57:42: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:42: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:42: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:42: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:42: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 10:57:42: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 02 Aug 2022 10:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.20_model.r WARNING @ Tue, 02 Aug 2022 10:57:42: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:57:42: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 02 Aug 2022 10:57:42: #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 10:57:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:57:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110365/SRX13110365.20_summits.bed INFO @ Tue, 02 Aug 2022 10:58:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 19 millis CompletedMACS2peakCalling