Job ID = 14167184 SRX = SRX11541635 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-10T01:48:39 prefetch.2.10.7: 1) Downloading 'SRR15235733'... 2021-12-10T01:48:39 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T01:49:42 prefetch.2.10.7: HTTPS download succeed 2021-12-10T01:49:42 prefetch.2.10.7: 1) 'SRR15235733' was downloaded successfully 2021-12-10T01:49:42 prefetch.2.10.7: 'SRR15235733' has 0 unresolved dependencies Read 15601452 spots for SRR15235733/SRR15235733.sra Written 15601452 spots for SRR15235733/SRR15235733.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167735 ("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: 00:07:39 15601452 reads; of these: 15601452 (100.00%) were unpaired; of these: 8615649 (55.22%) aligned 0 times 5907683 (37.87%) aligned exactly 1 time 1078120 (6.91%) aligned >1 times 44.78% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 5215676 / 6985803 = 0.7466 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.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 @ Fri, 10 Dec 2021 11:00:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:46: 1000000 INFO @ Fri, 10 Dec 2021 11:00:52: #1 tag size is determined as 101 bps INFO @ Fri, 10 Dec 2021 11:00:52: #1 tag size = 101 INFO @ Fri, 10 Dec 2021 11:00:52: #1 total tags in treatment: 1770127 INFO @ Fri, 10 Dec 2021 11:00:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:00:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:00:52: #1 tags after filtering in treatment: 1770127 INFO @ Fri, 10 Dec 2021 11:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:00:52: #1 finished! INFO @ Fri, 10 Dec 2021 11:00:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:00:52: #2 number of paired peaks: 1304 INFO @ Fri, 10 Dec 2021 11:00:52: start model_add_line... INFO @ Fri, 10 Dec 2021 11:00:52: start X-correlation... INFO @ Fri, 10 Dec 2021 11:00:52: end of X-cor INFO @ Fri, 10 Dec 2021 11:00:52: #2 finished! INFO @ Fri, 10 Dec 2021 11:00:52: #2 predicted fragment length is 109 bps INFO @ Fri, 10 Dec 2021 11:00:52: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 10 Dec 2021 11:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.05_model.r WARNING @ Fri, 10 Dec 2021 11:00:52: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:00:52: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Fri, 10 Dec 2021 11:00:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:00:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:00:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:00:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:00:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:00:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.05_summits.bed INFO @ Fri, 10 Dec 2021 11:00:58: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2549 records, 4 fields): 4 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.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 @ Fri, 10 Dec 2021 11:01:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:16: 1000000 INFO @ Fri, 10 Dec 2021 11:01:22: #1 tag size is determined as 101 bps INFO @ Fri, 10 Dec 2021 11:01:22: #1 tag size = 101 INFO @ Fri, 10 Dec 2021 11:01:22: #1 total tags in treatment: 1770127 INFO @ Fri, 10 Dec 2021 11:01:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:01:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:01:22: #1 tags after filtering in treatment: 1770127 INFO @ Fri, 10 Dec 2021 11:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:01:22: #1 finished! INFO @ Fri, 10 Dec 2021 11:01:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:01:22: #2 number of paired peaks: 1304 INFO @ Fri, 10 Dec 2021 11:01:22: start model_add_line... INFO @ Fri, 10 Dec 2021 11:01:22: start X-correlation... INFO @ Fri, 10 Dec 2021 11:01:22: end of X-cor INFO @ Fri, 10 Dec 2021 11:01:22: #2 finished! INFO @ Fri, 10 Dec 2021 11:01:22: #2 predicted fragment length is 109 bps INFO @ Fri, 10 Dec 2021 11:01:22: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 10 Dec 2021 11:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.10_model.r WARNING @ Fri, 10 Dec 2021 11:01:22: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:01:22: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Fri, 10 Dec 2021 11:01:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:01:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:01:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.10_summits.bed INFO @ Fri, 10 Dec 2021 11:01:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (971 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.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 @ Fri, 10 Dec 2021 11:01:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:47: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:01:53: #1 tag size is determined as 101 bps INFO @ Fri, 10 Dec 2021 11:01:53: #1 tag size = 101 INFO @ Fri, 10 Dec 2021 11:01:53: #1 total tags in treatment: 1770127 INFO @ Fri, 10 Dec 2021 11:01:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:01:53: #1 tags after filtering in treatment: 1770127 INFO @ Fri, 10 Dec 2021 11:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:01:53: #1 finished! INFO @ Fri, 10 Dec 2021 11:01:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:01:53: #2 number of paired peaks: 1304 INFO @ Fri, 10 Dec 2021 11:01:53: start model_add_line... INFO @ Fri, 10 Dec 2021 11:01:53: start X-correlation... INFO @ Fri, 10 Dec 2021 11:01:53: end of X-cor INFO @ Fri, 10 Dec 2021 11:01:53: #2 finished! INFO @ Fri, 10 Dec 2021 11:01:53: #2 predicted fragment length is 109 bps INFO @ Fri, 10 Dec 2021 11:01:53: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 10 Dec 2021 11:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.20_model.r WARNING @ Fri, 10 Dec 2021 11:01:53: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:01:53: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Fri, 10 Dec 2021 11:01:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:01:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:01:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11541635/SRX11541635.20_summits.bed INFO @ Fri, 10 Dec 2021 11:01:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (391 records, 4 fields): 1 millis CompletedMACS2peakCalling