Job ID = 16435588 SRX = SRX13110371 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:49:46 prefetch.2.10.7: 1) Downloading 'SRR16918041'... 2022-08-02T01:49:46 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:50:21 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:50:21 prefetch.2.10.7: 1) 'SRR16918041' was downloaded successfully 2022-08-02T01:50:21 prefetch.2.10.7: 'SRR16918041' has 0 unresolved dependencies Read 20031860 spots for SRR16918041/SRR16918041.sra Written 20031860 spots for SRR16918041/SRR16918041.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436139 ("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: 00:02:12 20031860 reads; of these: 20031860 (100.00%) were unpaired; of these: 18267685 (91.19%) aligned 0 times 1500218 (7.49%) aligned exactly 1 time 263957 (1.32%) aligned >1 times 8.81% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 94282 / 1764175 = 0.0534 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 10:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.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 10:54:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:54:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:54:44: 1000000 INFO @ Tue, 02 Aug 2022 10:54:48: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:48: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:48: #1 total tags in treatment: 1669893 INFO @ Tue, 02 Aug 2022 10:54:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:48: #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 10:54:48: #1 tags after filtering in treatment: 1669893 INFO @ Tue, 02 Aug 2022 10:54:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:48: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:48: #2 number of paired peaks: 283 WARNING @ Tue, 02 Aug 2022 10:54:48: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Tue, 02 Aug 2022 10:54:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:48: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:54:48: #2 alternative fragment length(s) may be 74,449,483,520,541 bps INFO @ Tue, 02 Aug 2022 10:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.05_model.r WARNING @ Tue, 02 Aug 2022 10:54:48: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:54:48: #2 You may need to consider one of the other alternative d(s): 74,449,483,520,541 WARNING @ Tue, 02 Aug 2022 10:54:48: #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 10:54:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:54:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.05_summits.bed INFO @ Tue, 02 Aug 2022 10:54:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 235 millis CompletedMACS2peakCalling 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 10:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.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 10:55:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:55:15: 1000000 INFO @ Tue, 02 Aug 2022 10:55:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:55:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:55:19: #1 total tags in treatment: 1669893 INFO @ Tue, 02 Aug 2022 10:55:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:55:19: #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 10:55:19: #1 tags after filtering in treatment: 1669893 INFO @ Tue, 02 Aug 2022 10:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:55:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:55:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:55:19: #2 number of paired peaks: 283 WARNING @ Tue, 02 Aug 2022 10:55:19: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Tue, 02 Aug 2022 10:55:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:55:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:55:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:55:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:55:19: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:55:19: #2 alternative fragment length(s) may be 74,449,483,520,541 bps INFO @ Tue, 02 Aug 2022 10:55:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.10_model.r WARNING @ Tue, 02 Aug 2022 10:55:19: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:55:19: #2 You may need to consider one of the other alternative d(s): 74,449,483,520,541 WARNING @ Tue, 02 Aug 2022 10:55:19: #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 10:55:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:55:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:55:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.10_summits.bed INFO @ Tue, 02 Aug 2022 10:55:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (132 records, 4 fields): 38 millis CompletedMACS2peakCalling 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 10:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.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 10:55:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:37: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:55:44: 1000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:55:48: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:55:48: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:55:48: #1 total tags in treatment: 1669893 INFO @ Tue, 02 Aug 2022 10:55:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:55:48: #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 10:55:48: #1 tags after filtering in treatment: 1669893 INFO @ Tue, 02 Aug 2022 10:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:55:48: #1 finished! INFO @ Tue, 02 Aug 2022 10:55:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:55:49: #2 number of paired peaks: 283 WARNING @ Tue, 02 Aug 2022 10:55:49: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Tue, 02 Aug 2022 10:55:49: start model_add_line... INFO @ Tue, 02 Aug 2022 10:55:49: start X-correlation... INFO @ Tue, 02 Aug 2022 10:55:49: end of X-cor INFO @ Tue, 02 Aug 2022 10:55:49: #2 finished! INFO @ Tue, 02 Aug 2022 10:55:49: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:55:49: #2 alternative fragment length(s) may be 74,449,483,520,541 bps INFO @ Tue, 02 Aug 2022 10:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.20_model.r WARNING @ Tue, 02 Aug 2022 10:55:49: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:55:49: #2 You may need to consider one of the other alternative d(s): 74,449,483,520,541 WARNING @ Tue, 02 Aug 2022 10:55:49: #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 10:55:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:55:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110371/SRX13110371.20_summits.bed INFO @ Tue, 02 Aug 2022 10:55:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 16 millis CompletedMACS2peakCalling