Job ID = 16436280 SRX = ERX9180702 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:21:09 prefetch.2.10.7: 1) Downloading 'ERR9627610'... 2022-08-02T02:21:09 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:23:00 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:23:00 prefetch.2.10.7: 1) 'ERR9627610' was downloaded successfully 2022-08-02T02:23:00 prefetch.2.10.7: 'ERR9627610' has 0 unresolved dependencies Read 28132246 spots for ERR9627610/ERR9627610.sra Written 28132246 spots for ERR9627610/ERR9627610.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436854 ("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: 00:30:10 28132246 reads; of these: 28132246 (100.00%) were paired; of these: 14692076 (52.23%) aligned concordantly 0 times 10977525 (39.02%) aligned concordantly exactly 1 time 2462645 (8.75%) aligned concordantly >1 times ---- 14692076 pairs aligned concordantly 0 times; of these: 891174 (6.07%) aligned discordantly 1 time ---- 13800902 pairs aligned 0 times concordantly or discordantly; of these: 27601804 mates make up the pairs; of these: 24466476 (88.64%) aligned 0 times 2245194 (8.13%) aligned exactly 1 time 890134 (3.22%) aligned >1 times 56.52% overall alignment rate Time searching: 00:30:10 Overall time: 00:30:10 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2151520 / 12818772 = 0.1678 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 12:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.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 12:05:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:05:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:06:04: 1000000 INFO @ Tue, 02 Aug 2022 12:06:10: 2000000 INFO @ Tue, 02 Aug 2022 12:06:15: 3000000 INFO @ Tue, 02 Aug 2022 12:06:21: 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 12:06:27: 5000000 INFO @ Tue, 02 Aug 2022 12:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.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 12:06:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:06:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:06:35: 6000000 INFO @ Tue, 02 Aug 2022 12:06:36: 1000000 INFO @ Tue, 02 Aug 2022 12:06:43: 7000000 INFO @ Tue, 02 Aug 2022 12:06:45: 2000000 INFO @ Tue, 02 Aug 2022 12:06:51: 8000000 INFO @ Tue, 02 Aug 2022 12:06:53: 3000000 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 12:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.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 12:06:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:06:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:06:59: 9000000 INFO @ Tue, 02 Aug 2022 12:07:02: 4000000 INFO @ Tue, 02 Aug 2022 12:07:06: 1000000 INFO @ Tue, 02 Aug 2022 12:07:08: 10000000 INFO @ Tue, 02 Aug 2022 12:07:09: 5000000 INFO @ Tue, 02 Aug 2022 12:07:14: 2000000 INFO @ Tue, 02 Aug 2022 12:07:16: 11000000 INFO @ Tue, 02 Aug 2022 12:07:17: 6000000 INFO @ Tue, 02 Aug 2022 12:07:22: 3000000 INFO @ Tue, 02 Aug 2022 12:07:24: 12000000 INFO @ Tue, 02 Aug 2022 12:07:26: 7000000 INFO @ Tue, 02 Aug 2022 12:07:29: 4000000 INFO @ Tue, 02 Aug 2022 12:07:32: 13000000 INFO @ Tue, 02 Aug 2022 12:07:33: 8000000 INFO @ Tue, 02 Aug 2022 12:07:37: 5000000 INFO @ Tue, 02 Aug 2022 12:07:40: 14000000 INFO @ Tue, 02 Aug 2022 12:07:42: 9000000 INFO @ Tue, 02 Aug 2022 12:07:45: 6000000 INFO @ Tue, 02 Aug 2022 12:07:48: 15000000 INFO @ Tue, 02 Aug 2022 12:07:50: 10000000 INFO @ Tue, 02 Aug 2022 12:07:52: 7000000 INFO @ Tue, 02 Aug 2022 12:07:56: 16000000 INFO @ Tue, 02 Aug 2022 12:07:58: 11000000 INFO @ Tue, 02 Aug 2022 12:08:00: 8000000 INFO @ Tue, 02 Aug 2022 12:08:04: 17000000 INFO @ Tue, 02 Aug 2022 12:08:05: 12000000 INFO @ Tue, 02 Aug 2022 12:08:07: 9000000 INFO @ Tue, 02 Aug 2022 12:08:12: 18000000 INFO @ Tue, 02 Aug 2022 12:08:13: 13000000 INFO @ Tue, 02 Aug 2022 12:08:15: 10000000 INFO @ Tue, 02 Aug 2022 12:08:20: 19000000 INFO @ Tue, 02 Aug 2022 12:08:22: 14000000 INFO @ Tue, 02 Aug 2022 12:08:23: 11000000 INFO @ Tue, 02 Aug 2022 12:08:28: 20000000 INFO @ Tue, 02 Aug 2022 12:08:30: 15000000 INFO @ Tue, 02 Aug 2022 12:08:31: 12000000 INFO @ Tue, 02 Aug 2022 12:08:35: 21000000 INFO @ Tue, 02 Aug 2022 12:08:38: 13000000 INFO @ Tue, 02 Aug 2022 12:08:39: 16000000 INFO @ Tue, 02 Aug 2022 12:08:43: 22000000 INFO @ Tue, 02 Aug 2022 12:08:45: 14000000 INFO @ Tue, 02 Aug 2022 12:08:47: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:08:51: 23000000 INFO @ Tue, 02 Aug 2022 12:08:53: 15000000 INFO @ Tue, 02 Aug 2022 12:08:54: 18000000 INFO @ Tue, 02 Aug 2022 12:08:58: 24000000 INFO @ Tue, 02 Aug 2022 12:09:00: 16000000 INFO @ Tue, 02 Aug 2022 12:09:02: 19000000 INFO @ Tue, 02 Aug 2022 12:09:06: 25000000 INFO @ Tue, 02 Aug 2022 12:09:08: 17000000 INFO @ Tue, 02 Aug 2022 12:09:09: 20000000 INFO @ Tue, 02 Aug 2022 12:09:14: 26000000 INFO @ Tue, 02 Aug 2022 12:09:16: 18000000 INFO @ Tue, 02 Aug 2022 12:09:16: 21000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:09:22: 27000000 INFO @ Tue, 02 Aug 2022 12:09:23: 19000000 INFO @ Tue, 02 Aug 2022 12:09:24: 22000000 INFO @ Tue, 02 Aug 2022 12:09:26: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 12:09:26: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 12:09:26: #1 total tags in treatment: 11431720 INFO @ Tue, 02 Aug 2022 12:09:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:09:26: #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 12:09:26: #1 tags after filtering in treatment: 9480261 INFO @ Tue, 02 Aug 2022 12:09:26: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 02 Aug 2022 12:09:26: #1 finished! INFO @ Tue, 02 Aug 2022 12:09:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:09:27: #2 number of paired peaks: 9890 INFO @ Tue, 02 Aug 2022 12:09:27: start model_add_line... INFO @ Tue, 02 Aug 2022 12:09:27: start X-correlation... INFO @ Tue, 02 Aug 2022 12:09:27: end of X-cor INFO @ Tue, 02 Aug 2022 12:09:27: #2 finished! INFO @ Tue, 02 Aug 2022 12:09:27: #2 predicted fragment length is 105 bps INFO @ Tue, 02 Aug 2022 12:09:27: #2 alternative fragment length(s) may be 105,598 bps INFO @ Tue, 02 Aug 2022 12:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.05_model.r WARNING @ Tue, 02 Aug 2022 12:09:27: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:09:27: #2 You may need to consider one of the other alternative d(s): 105,598 WARNING @ Tue, 02 Aug 2022 12:09:27: #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 12:09:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:09:31: 20000000 INFO @ Tue, 02 Aug 2022 12:09:31: 23000000 INFO @ Tue, 02 Aug 2022 12:09:38: 21000000 INFO @ Tue, 02 Aug 2022 12:09:39: 24000000 INFO @ Tue, 02 Aug 2022 12:09:46: 22000000 INFO @ Tue, 02 Aug 2022 12:09:46: 25000000 INFO @ Tue, 02 Aug 2022 12:09:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:09:53: 26000000 INFO @ Tue, 02 Aug 2022 12:09:54: 23000000 INFO @ Tue, 02 Aug 2022 12:10:01: 27000000 INFO @ Tue, 02 Aug 2022 12:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:10:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.05_summits.bed INFO @ Tue, 02 Aug 2022 12:10:01: Done! INFO @ Tue, 02 Aug 2022 12:10:01: 24000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9247 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:10:05: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 12:10:05: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 12:10:05: #1 total tags in treatment: 11431720 INFO @ Tue, 02 Aug 2022 12:10:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:10:05: #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 12:10:05: #1 tags after filtering in treatment: 9480261 INFO @ Tue, 02 Aug 2022 12:10:05: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 02 Aug 2022 12:10:05: #1 finished! INFO @ Tue, 02 Aug 2022 12:10:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:10:06: #2 number of paired peaks: 9890 INFO @ Tue, 02 Aug 2022 12:10:06: start model_add_line... INFO @ Tue, 02 Aug 2022 12:10:06: start X-correlation... INFO @ Tue, 02 Aug 2022 12:10:06: end of X-cor INFO @ Tue, 02 Aug 2022 12:10:06: #2 finished! INFO @ Tue, 02 Aug 2022 12:10:06: #2 predicted fragment length is 105 bps INFO @ Tue, 02 Aug 2022 12:10:06: #2 alternative fragment length(s) may be 105,598 bps INFO @ Tue, 02 Aug 2022 12:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.10_model.r WARNING @ Tue, 02 Aug 2022 12:10:06: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:10:06: #2 You may need to consider one of the other alternative d(s): 105,598 WARNING @ Tue, 02 Aug 2022 12:10:06: #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 12:10:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:10:08: 25000000 INFO @ Tue, 02 Aug 2022 12:10:15: 26000000 INFO @ Tue, 02 Aug 2022 12:10:21: 27000000 INFO @ Tue, 02 Aug 2022 12:10:24: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 12:10:24: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 12:10:24: #1 total tags in treatment: 11431720 INFO @ Tue, 02 Aug 2022 12:10:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:10:24: #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 12:10:25: #1 tags after filtering in treatment: 9480261 INFO @ Tue, 02 Aug 2022 12:10:25: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 02 Aug 2022 12:10:25: #1 finished! INFO @ Tue, 02 Aug 2022 12:10:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:10:26: #2 number of paired peaks: 9890 INFO @ Tue, 02 Aug 2022 12:10:26: start model_add_line... INFO @ Tue, 02 Aug 2022 12:10:26: start X-correlation... INFO @ Tue, 02 Aug 2022 12:10:26: end of X-cor INFO @ Tue, 02 Aug 2022 12:10:26: #2 finished! INFO @ Tue, 02 Aug 2022 12:10:26: #2 predicted fragment length is 105 bps INFO @ Tue, 02 Aug 2022 12:10:26: #2 alternative fragment length(s) may be 105,598 bps INFO @ Tue, 02 Aug 2022 12:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.20_model.r WARNING @ Tue, 02 Aug 2022 12:10:26: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:10:26: #2 You may need to consider one of the other alternative d(s): 105,598 WARNING @ Tue, 02 Aug 2022 12:10:26: #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 12:10:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:10:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.10_summits.bed INFO @ Tue, 02 Aug 2022 12:10:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7928 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:10:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180702/ERX9180702.20_summits.bed INFO @ Tue, 02 Aug 2022 12:10:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5670 records, 4 fields): 26 millis CompletedMACS2peakCalling