Job ID = 16439289 SRX = SRX15206480 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:50:35 prefetch.2.10.7: 1) Downloading 'SRR19139323'... 2022-08-02T05:50:35 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:51:01 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:51:02 prefetch.2.10.7: 'SRR19139323' is valid 2022-08-02T05:51:02 prefetch.2.10.7: 1) 'SRR19139323' was downloaded successfully 2022-08-02T05:51:02 prefetch.2.10.7: 'SRR19139323' has 0 unresolved dependencies Read 12634248 spots for SRR19139323/SRR19139323.sra Written 12634248 spots for SRR19139323/SRR19139323.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439388 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:15 12634248 reads; of these: 12634248 (100.00%) were unpaired; of these: 2296172 (18.17%) aligned 0 times 5705280 (45.16%) aligned exactly 1 time 4632796 (36.67%) aligned >1 times 81.83% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6476956 / 10338076 = 0.6265 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 15:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.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 15:03:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:03:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:03:47: 1000000 INFO @ Tue, 02 Aug 2022 15:03:58: 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 15:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.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 15:04:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:04:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:09: 3000000 INFO @ Tue, 02 Aug 2022 15:04:15: 1000000 INFO @ Tue, 02 Aug 2022 15:04:19: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 15:04:19: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 15:04:19: #1 total tags in treatment: 3861120 INFO @ Tue, 02 Aug 2022 15:04:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:04:19: #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 15:04:19: #1 tags after filtering in treatment: 3861120 INFO @ Tue, 02 Aug 2022 15:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:04:19: #1 finished! INFO @ Tue, 02 Aug 2022 15:04:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:04:20: #2 number of paired peaks: 6795 INFO @ Tue, 02 Aug 2022 15:04:20: start model_add_line... INFO @ Tue, 02 Aug 2022 15:04:20: start X-correlation... INFO @ Tue, 02 Aug 2022 15:04:20: end of X-cor INFO @ Tue, 02 Aug 2022 15:04:20: #2 finished! INFO @ Tue, 02 Aug 2022 15:04:20: #2 predicted fragment length is 136 bps INFO @ Tue, 02 Aug 2022 15:04:20: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 02 Aug 2022 15:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.05_model.r WARNING @ Tue, 02 Aug 2022 15:04:20: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:04:20: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 02 Aug 2022 15:04:20: #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 15:04:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:04:26: 2000000 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 15:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.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 15:04:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:04:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:04:37: 3000000 INFO @ Tue, 02 Aug 2022 15:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.05_summits.bed INFO @ Tue, 02 Aug 2022 15:04:43: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8093 records, 4 fields): 107 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:04:46: 1000000 INFO @ Tue, 02 Aug 2022 15:04:47: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 15:04:47: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 15:04:47: #1 total tags in treatment: 3861120 INFO @ Tue, 02 Aug 2022 15:04:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:04:47: #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 15:04:47: #1 tags after filtering in treatment: 3861120 INFO @ Tue, 02 Aug 2022 15:04:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:04:47: #1 finished! INFO @ Tue, 02 Aug 2022 15:04:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:04:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:04:48: #2 number of paired peaks: 6795 INFO @ Tue, 02 Aug 2022 15:04:48: start model_add_line... INFO @ Tue, 02 Aug 2022 15:04:48: start X-correlation... INFO @ Tue, 02 Aug 2022 15:04:48: end of X-cor INFO @ Tue, 02 Aug 2022 15:04:48: #2 finished! INFO @ Tue, 02 Aug 2022 15:04:48: #2 predicted fragment length is 136 bps INFO @ Tue, 02 Aug 2022 15:04:48: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 02 Aug 2022 15:04:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.10_model.r WARNING @ Tue, 02 Aug 2022 15:04:48: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:04:48: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 02 Aug 2022 15:04:48: #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 15:04:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:04:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:04:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:05:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:05:08: 3000000 INFO @ Tue, 02 Aug 2022 15:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.10_summits.bed INFO @ Tue, 02 Aug 2022 15:05:09: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5470 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:05:17: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 15:05:17: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 15:05:17: #1 total tags in treatment: 3861120 INFO @ Tue, 02 Aug 2022 15:05:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:05:17: #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 15:05:17: #1 tags after filtering in treatment: 3861120 INFO @ Tue, 02 Aug 2022 15:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:05:17: #1 finished! INFO @ Tue, 02 Aug 2022 15:05:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:05:18: #2 number of paired peaks: 6795 INFO @ Tue, 02 Aug 2022 15:05:18: start model_add_line... INFO @ Tue, 02 Aug 2022 15:05:18: start X-correlation... INFO @ Tue, 02 Aug 2022 15:05:18: end of X-cor INFO @ Tue, 02 Aug 2022 15:05:18: #2 finished! INFO @ Tue, 02 Aug 2022 15:05:18: #2 predicted fragment length is 136 bps INFO @ Tue, 02 Aug 2022 15:05:18: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 02 Aug 2022 15:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.20_model.r WARNING @ Tue, 02 Aug 2022 15:05:18: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:05:18: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 02 Aug 2022 15:05:18: #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 15:05:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:05:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206480/SRX15206480.20_summits.bed INFO @ Tue, 02 Aug 2022 15:05:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2771 records, 4 fields): 31 millis CompletedMACS2peakCalling