Job ID = 16439173 SRX = SRX15206456 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:42:45 prefetch.2.10.7: 1) Downloading 'SRR19139350'... 2022-08-02T05:42:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:43:04 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:43:04 prefetch.2.10.7: 'SRR19139350' is valid 2022-08-02T05:43:04 prefetch.2.10.7: 1) 'SRR19139350' was downloaded successfully 2022-08-02T05:43:04 prefetch.2.10.7: 'SRR19139350' has 0 unresolved dependencies Read 9678551 spots for SRR19139350/SRR19139350.sra Written 9678551 spots for SRR19139350/SRR19139350.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439283 ("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: 00:03:17 9678551 reads; of these: 9678551 (100.00%) were unpaired; of these: 5285122 (54.61%) aligned 0 times 3267612 (33.76%) aligned exactly 1 time 1125817 (11.63%) aligned >1 times 45.39% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 442577 / 4393429 = 0.1007 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 14:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.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 14:49:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:23: 1000000 INFO @ Tue, 02 Aug 2022 14:49:33: 2000000 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 14:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.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 14:49:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:43: 3000000 INFO @ Tue, 02 Aug 2022 14:49:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:49:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:49:53: #1 total tags in treatment: 3950852 INFO @ Tue, 02 Aug 2022 14:49:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:53: #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 14:49:53: #1 tags after filtering in treatment: 3950852 INFO @ Tue, 02 Aug 2022 14:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:53: 1000000 INFO @ Tue, 02 Aug 2022 14:49:53: #2 number of paired peaks: 1938 INFO @ Tue, 02 Aug 2022 14:49:53: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:54: #2 predicted fragment length is 145 bps INFO @ Tue, 02 Aug 2022 14:49:54: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 02 Aug 2022 14:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.05_model.r WARNING @ Tue, 02 Aug 2022 14:49:54: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:49:54: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Tue, 02 Aug 2022 14:49:54: #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 14:49:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:03: 2000000 INFO @ Tue, 02 Aug 2022 14:50:07: #3 Call peaks for each chromosome... 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 14:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.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 14:50:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:14: 3000000 INFO @ Tue, 02 Aug 2022 14:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.05_summits.bed INFO @ Tue, 02 Aug 2022 14:50:14: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4223 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:23: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:50:23: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:50:23: #1 total tags in treatment: 3950852 INFO @ Tue, 02 Aug 2022 14:50:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:23: #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 14:50:23: #1 tags after filtering in treatment: 3950852 INFO @ Tue, 02 Aug 2022 14:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:23: 1000000 INFO @ Tue, 02 Aug 2022 14:50:23: #2 number of paired peaks: 1938 INFO @ Tue, 02 Aug 2022 14:50:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:23: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:23: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:23: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:23: #2 predicted fragment length is 145 bps INFO @ Tue, 02 Aug 2022 14:50:23: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 02 Aug 2022 14:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.10_model.r WARNING @ Tue, 02 Aug 2022 14:50:23: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:23: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Tue, 02 Aug 2022 14:50:23: #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 14:50:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:33: 2000000 INFO @ Tue, 02 Aug 2022 14:50:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:50:43: 3000000 INFO @ Tue, 02 Aug 2022 14:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2094 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:50:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:50:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:50:53: #1 total tags in treatment: 3950852 INFO @ Tue, 02 Aug 2022 14:50:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:53: #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 14:50:53: #1 tags after filtering in treatment: 3950852 INFO @ Tue, 02 Aug 2022 14:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:54: #2 number of paired peaks: 1938 INFO @ Tue, 02 Aug 2022 14:50:54: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:54: #2 predicted fragment length is 145 bps INFO @ Tue, 02 Aug 2022 14:50:54: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 02 Aug 2022 14:50:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.20_model.r WARNING @ Tue, 02 Aug 2022 14:50:54: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:54: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Tue, 02 Aug 2022 14:50:54: #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 14:50:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:51:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206456/SRX15206456.20_summits.bed INFO @ Tue, 02 Aug 2022 14:51:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (928 records, 4 fields): 19 millis CompletedMACS2peakCalling