Job ID = 16438945 SRX = SRX15206520 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:13:00 prefetch.2.10.7: 1) Downloading 'SRR19139272'... 2022-08-02T05:13:00 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:13:08 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:13:09 prefetch.2.10.7: 'SRR19139272' is valid 2022-08-02T05:13:09 prefetch.2.10.7: 1) 'SRR19139272' was downloaded successfully 2022-08-02T05:13:09 prefetch.2.10.7: 'SRR19139272' has 0 unresolved dependencies Read 2553680 spots for SRR19139272/SRR19139272.sra Written 2553680 spots for SRR19139272/SRR19139272.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438973 ("srTdm6") 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: 00:02:34 2553680 reads; of these: 2553680 (100.00%) were unpaired; of these: 595029 (23.30%) aligned 0 times 1324140 (51.85%) aligned exactly 1 time 634511 (24.85%) aligned >1 times 76.70% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 524060 / 1958651 = 0.2676 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 14:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:17:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:17:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:17:48: 1000000 INFO @ Tue, 02 Aug 2022 14:17:53: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:17:53: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:17:53: #1 total tags in treatment: 1434591 INFO @ Tue, 02 Aug 2022 14:17:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:17:53: #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 14:17:53: #1 tags after filtering in treatment: 1434591 INFO @ Tue, 02 Aug 2022 14:17:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:17:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:17:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:17:54: #2 number of paired peaks: 348 WARNING @ Tue, 02 Aug 2022 14:17:54: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 02 Aug 2022 14:17:54: start model_add_line... INFO @ Tue, 02 Aug 2022 14:17:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:17:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:17:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:17:54: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 14:17:54: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 14:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.05_model.r WARNING @ Tue, 02 Aug 2022 14:17:54: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:17:54: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 14:17:54: #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 14:17:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:17:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.05_peaks.narrowPeak 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 14:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.05_summits.bed INFO @ Tue, 02 Aug 2022 14:18:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (581 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:18:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:14: 1000000 INFO @ Tue, 02 Aug 2022 14:18:19: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:18:19: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:18:19: #1 total tags in treatment: 1434591 INFO @ Tue, 02 Aug 2022 14:18:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:19: #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 14:18:19: #1 tags after filtering in treatment: 1434591 INFO @ Tue, 02 Aug 2022 14:18:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:19: #2 number of paired peaks: 348 WARNING @ Tue, 02 Aug 2022 14:18:19: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:19: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:19: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:19: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:19: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:19: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 14:18:19: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 14:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.10_model.r WARNING @ Tue, 02 Aug 2022 14:18:19: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:19: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 14:18:19: #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 14:18:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.10_summits.bed INFO @ Tue, 02 Aug 2022 14:18:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 25 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 14:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:18:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:34: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:18:44: 1000000 INFO @ Tue, 02 Aug 2022 14:18:49: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:18:49: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:18:49: #1 total tags in treatment: 1434591 INFO @ Tue, 02 Aug 2022 14:18:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:49: #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 14:18:49: #1 tags after filtering in treatment: 1434591 INFO @ Tue, 02 Aug 2022 14:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:49: #2 number of paired peaks: 348 WARNING @ Tue, 02 Aug 2022 14:18:49: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:49: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:49: start X-correlation... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:18:49: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:49: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:49: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 14:18:49: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 14:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.20_model.r WARNING @ Tue, 02 Aug 2022 14:18:49: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:49: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 14:18:49: #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 14:18:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206520/SRX15206520.20_summits.bed INFO @ Tue, 02 Aug 2022 14:18:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 77 millis CompletedMACS2peakCalling