Job ID = 16439433 SRX = SRX11965413 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T06:09:25 prefetch.2.10.7: 1) Downloading 'SRR15668748'... 2022-08-02T06:09:25 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:09:41 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:09:42 prefetch.2.10.7: 'SRR15668748' is valid 2022-08-02T06:09:42 prefetch.2.10.7: 1) 'SRR15668748' was downloaded successfully 2022-08-02T06:09:42 prefetch.2.10.7: 'SRR15668748' has 0 unresolved dependencies Read 12722727 spots for SRR15668748/SRR15668748.sra Written 12722727 spots for SRR15668748/SRR15668748.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439472 ("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: 00:04:15 12722727 reads; of these: 12722727 (100.00%) were unpaired; of these: 4495588 (35.34%) aligned 0 times 5996008 (47.13%) aligned exactly 1 time 2231131 (17.54%) aligned >1 times 64.66% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 5221772 / 8227139 = 0.6347 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 15:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.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 15:16:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:16:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:05: 1000000 INFO @ Tue, 02 Aug 2022 15:17:13: 2000000 INFO @ Tue, 02 Aug 2022 15:17:20: 3000000 INFO @ Tue, 02 Aug 2022 15:17:20: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:17:20: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:17:20: #1 total tags in treatment: 3005367 INFO @ Tue, 02 Aug 2022 15:17:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:20: #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 15:17:20: #1 tags after filtering in treatment: 3005367 INFO @ Tue, 02 Aug 2022 15:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:20: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:21: #2 number of paired peaks: 1371 INFO @ Tue, 02 Aug 2022 15:17:21: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:21: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:21: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:21: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:21: #2 predicted fragment length is 53 bps INFO @ Tue, 02 Aug 2022 15:17:21: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 02 Aug 2022 15:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.05_model.r WARNING @ Tue, 02 Aug 2022 15:17:21: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:21: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 02 Aug 2022 15:17:21: #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 15:17:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:21: #3 Pre-compute pvalue-qvalue table... 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 15:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.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 15:17:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:17:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.05_summits.bed INFO @ Tue, 02 Aug 2022 15:17:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2992 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:17:35: 1000000 INFO @ Tue, 02 Aug 2022 15:17:44: 2000000 INFO @ Tue, 02 Aug 2022 15:17:52: 3000000 INFO @ Tue, 02 Aug 2022 15:17:52: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:17:52: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:17:52: #1 total tags in treatment: 3005367 INFO @ Tue, 02 Aug 2022 15:17:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:52: #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 15:17:52: #1 tags after filtering in treatment: 3005367 INFO @ Tue, 02 Aug 2022 15:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:52: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:53: #2 number of paired peaks: 1371 INFO @ Tue, 02 Aug 2022 15:17:53: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:53: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:53: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:53: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:53: #2 predicted fragment length is 53 bps INFO @ Tue, 02 Aug 2022 15:17:53: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 02 Aug 2022 15:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.10_model.r WARNING @ Tue, 02 Aug 2022 15:17:53: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:53: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 02 Aug 2022 15:17:53: #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 15:17:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:53: #3 Pre-compute pvalue-qvalue table... 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 15:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.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 15:17:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:17:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.10_summits.bed INFO @ Tue, 02 Aug 2022 15:18:03: Done! pass1 - making usageList (13 chroms): 7 millis pass2 - checking and writing primary data (2197 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:18:04: 1000000 INFO @ Tue, 02 Aug 2022 15:18:12: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:18:21: 3000000 INFO @ Tue, 02 Aug 2022 15:18:21: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:18:21: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:18:21: #1 total tags in treatment: 3005367 INFO @ Tue, 02 Aug 2022 15:18:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:18:21: #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 15:18:21: #1 tags after filtering in treatment: 3005367 INFO @ Tue, 02 Aug 2022 15:18:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:18:21: #1 finished! INFO @ Tue, 02 Aug 2022 15:18:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:18:21: #2 number of paired peaks: 1371 INFO @ Tue, 02 Aug 2022 15:18:21: start model_add_line... INFO @ Tue, 02 Aug 2022 15:18:21: start X-correlation... INFO @ Tue, 02 Aug 2022 15:18:21: end of X-cor INFO @ Tue, 02 Aug 2022 15:18:21: #2 finished! INFO @ Tue, 02 Aug 2022 15:18:21: #2 predicted fragment length is 53 bps INFO @ Tue, 02 Aug 2022 15:18:21: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 02 Aug 2022 15:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.20_model.r WARNING @ Tue, 02 Aug 2022 15:18:21: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:18:21: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 02 Aug 2022 15:18:21: #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 15:18:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:18:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:18:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965413/SRX11965413.20_summits.bed INFO @ Tue, 02 Aug 2022 15:18:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1545 records, 4 fields): 4 millis CompletedMACS2peakCalling