Job ID = 16439435 SRX = SRX11965414 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T06:09:58 prefetch.2.10.7: 1) Downloading 'SRR15668749'... 2022-08-02T06:09:58 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:10:14 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:10:15 prefetch.2.10.7: 'SRR15668749' is valid 2022-08-02T06:10:15 prefetch.2.10.7: 1) 'SRR15668749' was downloaded successfully 2022-08-02T06:10:15 prefetch.2.10.7: 'SRR15668749' has 0 unresolved dependencies Read 12221609 spots for SRR15668749/SRR15668749.sra Written 12221609 spots for SRR15668749/SRR15668749.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439470 ("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: 00:03:16 12221609 reads; of these: 12221609 (100.00%) were unpaired; of these: 3646137 (29.83%) aligned 0 times 6612169 (54.10%) aligned exactly 1 time 1963303 (16.06%) aligned >1 times 70.17% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 5032112 / 8575472 = 0.5868 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 15:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.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 15:16:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:16:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:16:36: 1000000 INFO @ Tue, 02 Aug 2022 15:16:42: 2000000 INFO @ Tue, 02 Aug 2022 15:16:49: 3000000 INFO @ Tue, 02 Aug 2022 15:16:53: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:16:53: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:16:53: #1 total tags in treatment: 3543360 INFO @ Tue, 02 Aug 2022 15:16:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:16:53: #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 15:16:53: #1 tags after filtering in treatment: 3543360 INFO @ Tue, 02 Aug 2022 15:16:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:16:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:16:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:16:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:16:53: #2 number of paired peaks: 1080 INFO @ Tue, 02 Aug 2022 15:16:53: start model_add_line... INFO @ Tue, 02 Aug 2022 15:16:53: start X-correlation... INFO @ Tue, 02 Aug 2022 15:16:53: end of X-cor INFO @ Tue, 02 Aug 2022 15:16:53: #2 finished! INFO @ Tue, 02 Aug 2022 15:16:53: #2 predicted fragment length is 57 bps INFO @ Tue, 02 Aug 2022 15:16:53: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 02 Aug 2022 15:16:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.05_model.r WARNING @ Tue, 02 Aug 2022 15:16:53: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:16:53: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 02 Aug 2022 15:16:53: #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 15:16:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:16:53: #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 15:16:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.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 15:16:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:16:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:17:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:17:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:17:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.05_summits.bed INFO @ Tue, 02 Aug 2022 15:17:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2775 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:17:07: 1000000 INFO @ Tue, 02 Aug 2022 15:17:14: 2000000 INFO @ Tue, 02 Aug 2022 15:17:22: 3000000 INFO @ Tue, 02 Aug 2022 15:17:26: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:17:26: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:17:26: #1 total tags in treatment: 3543360 INFO @ Tue, 02 Aug 2022 15:17:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:26: #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 15:17:26: #1 tags after filtering in treatment: 3543360 INFO @ Tue, 02 Aug 2022 15:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:26: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:26: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Tue, 02 Aug 2022 15:17:26: #2 number of paired peaks: 1080 INFO @ Tue, 02 Aug 2022 15:17:26: start model_add_line... 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: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:26: #2 predicted fragment length is 57 bps INFO @ Tue, 02 Aug 2022 15:17:26: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 02 Aug 2022 15:17:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.10_model.r WARNING @ Tue, 02 Aug 2022 15:17:26: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:26: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 02 Aug 2022 15:17:26: #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 15:17:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:17:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.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 15:17:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:17:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:17:36: 1000000 INFO @ Tue, 02 Aug 2022 15:17:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:17:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:17:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.10_summits.bed INFO @ Tue, 02 Aug 2022 15:17:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1998 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:17:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:17:50: 3000000 INFO @ Tue, 02 Aug 2022 15:17:53: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:17:53: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:17:53: #1 total tags in treatment: 3543360 INFO @ Tue, 02 Aug 2022 15:17:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:53: #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 15:17:54: #1 tags after filtering in treatment: 3543360 INFO @ Tue, 02 Aug 2022 15:17:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:54: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:54: #2 number of paired peaks: 1080 INFO @ Tue, 02 Aug 2022 15:17:54: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:54: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:54: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:54: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:54: #2 predicted fragment length is 57 bps INFO @ Tue, 02 Aug 2022 15:17:54: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 02 Aug 2022 15:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.20_model.r WARNING @ Tue, 02 Aug 2022 15:17:54: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:54: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 02 Aug 2022 15:17:54: #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 15:17:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:18:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965414/SRX11965414.20_summits.bed INFO @ Tue, 02 Aug 2022 15:18:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1184 records, 4 fields): 4 millis CompletedMACS2peakCalling