Job ID = 16436193 SRX = SRX15369016 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:03:25 prefetch.2.10.7: 1) Downloading 'SRR19308745'... 2022-08-02T02:03:25 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:04:02 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:04:02 prefetch.2.10.7: 1) 'SRR19308745' was downloaded successfully 2022-08-02T02:04:02 prefetch.2.10.7: 'SRR19308745' has 0 unresolved dependencies Read 18703134 spots for SRR19308745/SRR19308745.sra Written 18703134 spots for SRR19308745/SRR19308745.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436275 ("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: 00:10:21 18703134 reads; of these: 18703134 (100.00%) were unpaired; of these: 624327 (3.34%) aligned 0 times 11093915 (59.32%) aligned exactly 1 time 6984892 (37.35%) aligned >1 times 96.66% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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] 13079857 / 18078807 = 0.7235 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 11:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.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 11:19:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:19:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:19:19: 1000000 INFO @ Tue, 02 Aug 2022 11:19:25: 2000000 INFO @ Tue, 02 Aug 2022 11:19:31: 3000000 INFO @ Tue, 02 Aug 2022 11:19:36: 4000000 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 11:19:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:19:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:19:42: #1 total tags in treatment: 4998950 INFO @ Tue, 02 Aug 2022 11:19:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:19:42: #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 11:19:42: #1 tags after filtering in treatment: 4998950 INFO @ Tue, 02 Aug 2022 11:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:19:42: #1 finished! INFO @ Tue, 02 Aug 2022 11:19:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:19:42: #2 number of paired peaks: 1106 INFO @ Tue, 02 Aug 2022 11:19:42: start model_add_line... INFO @ Tue, 02 Aug 2022 11:19:42: start X-correlation... INFO @ Tue, 02 Aug 2022 11:19:42: end of X-cor INFO @ Tue, 02 Aug 2022 11:19:42: #2 finished! INFO @ Tue, 02 Aug 2022 11:19:42: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:19:42: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 11:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.05_model.r WARNING @ Tue, 02 Aug 2022 11:19:42: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:19:42: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 11:19:42: #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 11:19:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.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 11:19:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:19:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:19:49: 1000000 INFO @ Tue, 02 Aug 2022 11:19:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:19:56: 2000000 INFO @ Tue, 02 Aug 2022 11:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.05_summits.bed INFO @ Tue, 02 Aug 2022 11:19:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5088 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:20:03: 3000000 INFO @ Tue, 02 Aug 2022 11:20:09: 4000000 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 11:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.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 11:20:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:20:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:20:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:20:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:20:16: #1 total tags in treatment: 4998950 INFO @ Tue, 02 Aug 2022 11:20:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:20:16: #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 11:20:16: #1 tags after filtering in treatment: 4998950 INFO @ Tue, 02 Aug 2022 11:20:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:20:16: #1 finished! INFO @ Tue, 02 Aug 2022 11:20:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:20:17: #2 number of paired peaks: 1106 INFO @ Tue, 02 Aug 2022 11:20:17: start model_add_line... INFO @ Tue, 02 Aug 2022 11:20:17: start X-correlation... INFO @ Tue, 02 Aug 2022 11:20:17: end of X-cor INFO @ Tue, 02 Aug 2022 11:20:17: #2 finished! INFO @ Tue, 02 Aug 2022 11:20:17: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:20:17: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 11:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.10_model.r WARNING @ Tue, 02 Aug 2022 11:20:17: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:20:17: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 11:20:17: #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 11:20:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:20:19: 1000000 INFO @ Tue, 02 Aug 2022 11:20:25: 2000000 INFO @ Tue, 02 Aug 2022 11:20:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:20:31: 3000000 INFO @ Tue, 02 Aug 2022 11:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.10_summits.bed INFO @ Tue, 02 Aug 2022 11:20:33: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1663 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:20:37: 4000000 INFO @ Tue, 02 Aug 2022 11:20:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:20:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:20:42: #1 total tags in treatment: 4998950 INFO @ Tue, 02 Aug 2022 11:20:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:20:42: #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 11:20:42: #1 tags after filtering in treatment: 4998950 INFO @ Tue, 02 Aug 2022 11:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:20:42: #1 finished! INFO @ Tue, 02 Aug 2022 11:20:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:20:43: #2 number of paired peaks: 1106 INFO @ Tue, 02 Aug 2022 11:20:43: start model_add_line... INFO @ Tue, 02 Aug 2022 11:20:43: start X-correlation... INFO @ Tue, 02 Aug 2022 11:20:43: end of X-cor INFO @ Tue, 02 Aug 2022 11:20:43: #2 finished! INFO @ Tue, 02 Aug 2022 11:20:43: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:20:43: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 11:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.20_model.r WARNING @ Tue, 02 Aug 2022 11:20:43: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:20:43: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 11:20:43: #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 11:20:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:20:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:20:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369016/SRX15369016.20_summits.bed INFO @ Tue, 02 Aug 2022 11:21:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 64 millis CompletedMACS2peakCalling