Job ID = 16440130 SRX = SRX12178820 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T08:18:53 prefetch.2.10.7: 1) Downloading 'SRR15888094'... 2022-08-02T08:18:53 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T08:20:33 prefetch.2.10.7: HTTPS download succeed 2022-08-02T08:20:33 prefetch.2.10.7: 1) 'SRR15888094' was downloaded successfully 2022-08-02T08:20:33 prefetch.2.10.7: 'SRR15888094' has 0 unresolved dependencies Read 32434840 spots for SRR15888094/SRR15888094.sra Written 32434840 spots for SRR15888094/SRR15888094.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440773 ("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: 00:24:52 32434840 reads; of these: 32434840 (100.00%) were paired; of these: 14279557 (44.03%) aligned concordantly 0 times 15591437 (48.07%) aligned concordantly exactly 1 time 2563846 (7.90%) aligned concordantly >1 times ---- 14279557 pairs aligned concordantly 0 times; of these: 3683720 (25.80%) aligned discordantly 1 time ---- 10595837 pairs aligned 0 times concordantly or discordantly; of these: 21191674 mates make up the pairs; of these: 17332599 (81.79%) aligned 0 times 2841499 (13.41%) aligned exactly 1 time 1017576 (4.80%) aligned >1 times 73.28% overall alignment rate Time searching: 00:24:52 Overall time: 00:24:52 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 20 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] 6081123 / 21738975 = 0.2797 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 17:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.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 17:58:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:58:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:58:22: 1000000 INFO @ Tue, 02 Aug 2022 17:58:27: 2000000 INFO @ Tue, 02 Aug 2022 17:58:31: 3000000 INFO @ Tue, 02 Aug 2022 17:58:36: 4000000 INFO @ Tue, 02 Aug 2022 17:58:41: 5000000 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 17:58:45: 6000000 INFO @ Tue, 02 Aug 2022 17:58:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.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 17:58:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:58:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:58:50: 7000000 INFO @ Tue, 02 Aug 2022 17:58:52: 1000000 INFO @ Tue, 02 Aug 2022 17:58:56: 8000000 INFO @ Tue, 02 Aug 2022 17:58:57: 2000000 INFO @ Tue, 02 Aug 2022 17:59:01: 9000000 INFO @ Tue, 02 Aug 2022 17:59:03: 3000000 INFO @ Tue, 02 Aug 2022 17:59:06: 10000000 INFO @ Tue, 02 Aug 2022 17:59:08: 4000000 INFO @ Tue, 02 Aug 2022 17:59:12: 11000000 INFO @ Tue, 02 Aug 2022 17:59:14: 5000000 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 17:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.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 17:59:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:59:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:59:17: 12000000 INFO @ Tue, 02 Aug 2022 17:59:19: 6000000 INFO @ Tue, 02 Aug 2022 17:59:23: 13000000 INFO @ Tue, 02 Aug 2022 17:59:23: 1000000 INFO @ Tue, 02 Aug 2022 17:59:25: 7000000 INFO @ Tue, 02 Aug 2022 17:59:29: 14000000 INFO @ Tue, 02 Aug 2022 17:59:29: 2000000 INFO @ Tue, 02 Aug 2022 17:59:31: 8000000 INFO @ Tue, 02 Aug 2022 17:59:35: 15000000 INFO @ Tue, 02 Aug 2022 17:59:36: 3000000 INFO @ Tue, 02 Aug 2022 17:59:37: 9000000 INFO @ Tue, 02 Aug 2022 17:59:40: 16000000 INFO @ Tue, 02 Aug 2022 17:59:42: 4000000 INFO @ Tue, 02 Aug 2022 17:59:43: 10000000 INFO @ Tue, 02 Aug 2022 17:59:46: 17000000 INFO @ Tue, 02 Aug 2022 17:59:48: 11000000 INFO @ Tue, 02 Aug 2022 17:59:49: 5000000 INFO @ Tue, 02 Aug 2022 17:59:52: 18000000 INFO @ Tue, 02 Aug 2022 17:59:54: 12000000 INFO @ Tue, 02 Aug 2022 17:59:55: 6000000 INFO @ Tue, 02 Aug 2022 17:59:58: 19000000 INFO @ Tue, 02 Aug 2022 18:00:00: 13000000 INFO @ Tue, 02 Aug 2022 18:00:01: 7000000 INFO @ Tue, 02 Aug 2022 18:00:04: 20000000 INFO @ Tue, 02 Aug 2022 18:00:06: 14000000 INFO @ Tue, 02 Aug 2022 18:00:07: 8000000 INFO @ Tue, 02 Aug 2022 18:00:10: 21000000 INFO @ Tue, 02 Aug 2022 18:00:12: 15000000 INFO @ Tue, 02 Aug 2022 18:00:14: 9000000 INFO @ Tue, 02 Aug 2022 18:00:15: 22000000 INFO @ Tue, 02 Aug 2022 18:00:18: 16000000 INFO @ Tue, 02 Aug 2022 18:00:20: 10000000 INFO @ Tue, 02 Aug 2022 18:00:21: 23000000 INFO @ Tue, 02 Aug 2022 18:00:23: 17000000 INFO @ Tue, 02 Aug 2022 18:00:26: 11000000 INFO @ Tue, 02 Aug 2022 18:00:27: 24000000 INFO @ Tue, 02 Aug 2022 18:00:29: 18000000 INFO @ Tue, 02 Aug 2022 18:00:32: 12000000 INFO @ Tue, 02 Aug 2022 18:00:33: 25000000 INFO @ Tue, 02 Aug 2022 18:00:35: 19000000 INFO @ Tue, 02 Aug 2022 18:00:39: 13000000 INFO @ Tue, 02 Aug 2022 18:00:39: 26000000 INFO @ Tue, 02 Aug 2022 18:00:41: 20000000 INFO @ Tue, 02 Aug 2022 18:00:45: 14000000 INFO @ Tue, 02 Aug 2022 18:00:45: 27000000 INFO @ Tue, 02 Aug 2022 18:00:46: 21000000 INFO @ Tue, 02 Aug 2022 18:00:51: 28000000 INFO @ Tue, 02 Aug 2022 18:00:51: 15000000 INFO @ Tue, 02 Aug 2022 18:00:52: 22000000 INFO @ Tue, 02 Aug 2022 18:00:57: 29000000 INFO @ Tue, 02 Aug 2022 18:00:57: 16000000 INFO @ Tue, 02 Aug 2022 18:00:58: 23000000 INFO @ Tue, 02 Aug 2022 18:01:03: 30000000 INFO @ Tue, 02 Aug 2022 18:01:03: 17000000 INFO @ Tue, 02 Aug 2022 18:01:04: 24000000 INFO @ Tue, 02 Aug 2022 18:01:09: 31000000 INFO @ Tue, 02 Aug 2022 18:01:09: 25000000 INFO @ Tue, 02 Aug 2022 18:01:09: 18000000 INFO @ Tue, 02 Aug 2022 18:01:14: 32000000 INFO @ Tue, 02 Aug 2022 18:01:15: 26000000 INFO @ Tue, 02 Aug 2022 18:01:16: 19000000 INFO @ Tue, 02 Aug 2022 18:01:20: 33000000 INFO @ Tue, 02 Aug 2022 18:01:21: 27000000 INFO @ Tue, 02 Aug 2022 18:01:22: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:01:26: 34000000 INFO @ Tue, 02 Aug 2022 18:01:27: 28000000 INFO @ Tue, 02 Aug 2022 18:01:28: 21000000 INFO @ Tue, 02 Aug 2022 18:01:32: 35000000 INFO @ Tue, 02 Aug 2022 18:01:33: 29000000 INFO @ Tue, 02 Aug 2022 18:01:34: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 18:01:34: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 18:01:34: #1 total tags in treatment: 12951578 INFO @ Tue, 02 Aug 2022 18:01:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:01:34: #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 18:01:34: 22000000 INFO @ Tue, 02 Aug 2022 18:01:34: #1 tags after filtering in treatment: 9698580 INFO @ Tue, 02 Aug 2022 18:01:34: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 18:01:34: #1 finished! INFO @ Tue, 02 Aug 2022 18:01:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:01:35: #2 number of paired peaks: 1849 INFO @ Tue, 02 Aug 2022 18:01:35: start model_add_line... INFO @ Tue, 02 Aug 2022 18:01:35: start X-correlation... INFO @ Tue, 02 Aug 2022 18:01:35: end of X-cor INFO @ Tue, 02 Aug 2022 18:01:35: #2 finished! INFO @ Tue, 02 Aug 2022 18:01:35: #2 predicted fragment length is 59 bps INFO @ Tue, 02 Aug 2022 18:01:35: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 02 Aug 2022 18:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.05_model.r WARNING @ Tue, 02 Aug 2022 18:01:35: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:01:35: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 02 Aug 2022 18:01:35: #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 18:01:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:01:39: 30000000 INFO @ Tue, 02 Aug 2022 18:01:40: 23000000 INFO @ Tue, 02 Aug 2022 18:01:44: 31000000 INFO @ Tue, 02 Aug 2022 18:01:46: 24000000 INFO @ Tue, 02 Aug 2022 18:01:50: 32000000 INFO @ Tue, 02 Aug 2022 18:01:53: 25000000 INFO @ Tue, 02 Aug 2022 18:01:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:01:56: 33000000 INFO @ Tue, 02 Aug 2022 18:01:59: 26000000 INFO @ Tue, 02 Aug 2022 18:02:02: 34000000 INFO @ Tue, 02 Aug 2022 18:02:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.05_summits.bed INFO @ Tue, 02 Aug 2022 18:02:05: Done! INFO @ Tue, 02 Aug 2022 18:02:05: 27000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14907 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:02:08: 35000000 INFO @ Tue, 02 Aug 2022 18:02:10: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 18:02:10: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 18:02:10: #1 total tags in treatment: 12951578 INFO @ Tue, 02 Aug 2022 18:02:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:02:10: #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 18:02:10: #1 tags after filtering in treatment: 9698580 INFO @ Tue, 02 Aug 2022 18:02:10: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 18:02:10: #1 finished! INFO @ Tue, 02 Aug 2022 18:02:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:02:11: #2 number of paired peaks: 1849 INFO @ Tue, 02 Aug 2022 18:02:11: start model_add_line... INFO @ Tue, 02 Aug 2022 18:02:11: start X-correlation... INFO @ Tue, 02 Aug 2022 18:02:11: end of X-cor INFO @ Tue, 02 Aug 2022 18:02:11: #2 finished! INFO @ Tue, 02 Aug 2022 18:02:11: #2 predicted fragment length is 59 bps INFO @ Tue, 02 Aug 2022 18:02:11: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 02 Aug 2022 18:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.10_model.r WARNING @ Tue, 02 Aug 2022 18:02:11: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:02:11: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 02 Aug 2022 18:02:11: #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 18:02:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:02:11: 28000000 INFO @ Tue, 02 Aug 2022 18:02:17: 29000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:02:23: 30000000 INFO @ Tue, 02 Aug 2022 18:02:28: 31000000 INFO @ Tue, 02 Aug 2022 18:02:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:02:34: 32000000 INFO @ Tue, 02 Aug 2022 18:02:40: 33000000 INFO @ Tue, 02 Aug 2022 18:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.10_summits.bed INFO @ Tue, 02 Aug 2022 18:02:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7058 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:02:45: 34000000 INFO @ Tue, 02 Aug 2022 18:02:51: 35000000 INFO @ Tue, 02 Aug 2022 18:02:53: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 18:02:53: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 18:02:53: #1 total tags in treatment: 12951578 INFO @ Tue, 02 Aug 2022 18:02:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:02:53: #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 18:02:53: #1 tags after filtering in treatment: 9698580 INFO @ Tue, 02 Aug 2022 18:02:53: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 18:02:53: #1 finished! INFO @ Tue, 02 Aug 2022 18:02:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:02:54: #2 number of paired peaks: 1849 INFO @ Tue, 02 Aug 2022 18:02:54: start model_add_line... INFO @ Tue, 02 Aug 2022 18:02:54: start X-correlation... INFO @ Tue, 02 Aug 2022 18:02:54: end of X-cor INFO @ Tue, 02 Aug 2022 18:02:54: #2 finished! INFO @ Tue, 02 Aug 2022 18:02:54: #2 predicted fragment length is 59 bps INFO @ Tue, 02 Aug 2022 18:02:54: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 02 Aug 2022 18:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.20_model.r WARNING @ Tue, 02 Aug 2022 18:02:54: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:02:54: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 02 Aug 2022 18:02:54: #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 18:02:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:03:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178820/SRX12178820.20_summits.bed INFO @ Tue, 02 Aug 2022 18:03:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 19 millis CompletedMACS2peakCalling