Job ID = 16436192 SRX = SRX15369015 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:03:10 prefetch.2.10.7: 1) Downloading 'SRR19308744'... 2022-08-02T02:03:10 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:03:41 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:03:42 prefetch.2.10.7: 'SRR19308744' is valid 2022-08-02T02:03:42 prefetch.2.10.7: 1) 'SRR19308744' was downloaded successfully 2022-08-02T02:03:42 prefetch.2.10.7: 'SRR19308744' has 0 unresolved dependencies Read 15629610 spots for SRR19308744/SRR19308744.sra Written 15629610 spots for SRR19308744/SRR19308744.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436268 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:12 15629610 reads; of these: 15629610 (100.00%) were unpaired; of these: 884115 (5.66%) aligned 0 times 10483102 (67.07%) aligned exactly 1 time 4262393 (27.27%) aligned >1 times 94.34% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12663232 / 14745495 = 0.8588 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 11:15:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.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 11:15:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:15:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:16:06: 1000000 INFO @ Tue, 02 Aug 2022 11:16:13: 2000000 INFO @ Tue, 02 Aug 2022 11:16:14: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:16:14: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:16:14: #1 total tags in treatment: 2082263 INFO @ Tue, 02 Aug 2022 11:16:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:16:14: #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 11:16:14: #1 tags after filtering in treatment: 2082263 INFO @ Tue, 02 Aug 2022 11:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:16:14: #1 finished! INFO @ Tue, 02 Aug 2022 11:16:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:16:14: #2 number of paired peaks: 4352 INFO @ Tue, 02 Aug 2022 11:16:14: start model_add_line... INFO @ Tue, 02 Aug 2022 11:16:14: start X-correlation... INFO @ Tue, 02 Aug 2022 11:16:14: end of X-cor INFO @ Tue, 02 Aug 2022 11:16:14: #2 finished! INFO @ Tue, 02 Aug 2022 11:16:14: #2 predicted fragment length is 85 bps INFO @ Tue, 02 Aug 2022 11:16:14: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 02 Aug 2022 11:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.05_model.r WARNING @ Tue, 02 Aug 2022 11:16:14: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:16:14: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Tue, 02 Aug 2022 11:16:14: #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 11:16:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:16:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:16:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:16:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:16:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.05_summits.bed INFO @ Tue, 02 Aug 2022 11:16:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2830 records, 4 fields): 45 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 11:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.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 11:16:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:16:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:16:35: 1000000 INFO @ Tue, 02 Aug 2022 11:16:42: 2000000 INFO @ Tue, 02 Aug 2022 11:16:43: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:16:43: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:16:43: #1 total tags in treatment: 2082263 INFO @ Tue, 02 Aug 2022 11:16:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:16:43: #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 11:16:43: #1 tags after filtering in treatment: 2082263 INFO @ Tue, 02 Aug 2022 11:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:16:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:16:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:16:43: #2 number of paired peaks: 4352 INFO @ Tue, 02 Aug 2022 11:16:43: start model_add_line... INFO @ Tue, 02 Aug 2022 11:16:43: start X-correlation... INFO @ Tue, 02 Aug 2022 11:16:43: end of X-cor INFO @ Tue, 02 Aug 2022 11:16:43: #2 finished! INFO @ Tue, 02 Aug 2022 11:16:43: #2 predicted fragment length is 85 bps INFO @ Tue, 02 Aug 2022 11:16:43: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 02 Aug 2022 11:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.10_model.r WARNING @ Tue, 02 Aug 2022 11:16:43: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:16:43: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Tue, 02 Aug 2022 11:16:43: #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 11:16:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:16:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.10_summits.bed INFO @ Tue, 02 Aug 2022 11:16:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (847 records, 4 fields): 23 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 11:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.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 11:16:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:16:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:17:04: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:17:12: 2000000 INFO @ Tue, 02 Aug 2022 11:17:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:17:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:17:13: #1 total tags in treatment: 2082263 INFO @ Tue, 02 Aug 2022 11:17:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:17:13: #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 11:17:13: #1 tags after filtering in treatment: 2082263 INFO @ Tue, 02 Aug 2022 11:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:17:13: #1 finished! INFO @ Tue, 02 Aug 2022 11:17:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:17:13: #2 number of paired peaks: 4352 INFO @ Tue, 02 Aug 2022 11:17:13: start model_add_line... INFO @ Tue, 02 Aug 2022 11:17:13: start X-correlation... INFO @ Tue, 02 Aug 2022 11:17:13: end of X-cor INFO @ Tue, 02 Aug 2022 11:17:13: #2 finished! INFO @ Tue, 02 Aug 2022 11:17:13: #2 predicted fragment length is 85 bps INFO @ Tue, 02 Aug 2022 11:17:13: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 02 Aug 2022 11:17:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.20_model.r WARNING @ Tue, 02 Aug 2022 11:17:13: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:17:13: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Tue, 02 Aug 2022 11:17:13: #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 11:17:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:17:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:17:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:17:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:17:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:17:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369015/SRX15369015.20_summits.bed INFO @ Tue, 02 Aug 2022 11:17:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 29 millis CompletedMACS2peakCalling