Job ID = 16436199 SRX = SRX12178852 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:04:28 prefetch.2.10.7: 1) Downloading 'SRR15888062'... 2022-08-02T02:04:28 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:06:38 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:06:38 prefetch.2.10.7: 1) 'SRR15888062' was downloaded successfully 2022-08-02T02:06:38 prefetch.2.10.7: 'SRR15888062' has 0 unresolved dependencies Read 49480954 spots for SRR15888062/SRR15888062.sra Written 49480954 spots for SRR15888062/SRR15888062.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436751 ("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: 00:27:59 49480954 reads; of these: 49480954 (100.00%) were paired; of these: 28851759 (58.31%) aligned concordantly 0 times 18156771 (36.69%) aligned concordantly exactly 1 time 2472424 (5.00%) aligned concordantly >1 times ---- 28851759 pairs aligned concordantly 0 times; of these: 3158849 (10.95%) aligned discordantly 1 time ---- 25692910 pairs aligned 0 times concordantly or discordantly; of these: 51385820 mates make up the pairs; of these: 48011236 (93.43%) aligned 0 times 2519116 (4.90%) aligned exactly 1 time 855468 (1.66%) aligned >1 times 51.49% overall alignment rate Time searching: 00:28:00 Overall time: 00:28:00 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 24 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] 8656807 / 23684819 = 0.3655 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 11:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.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 11:51:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:51:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:51:32: 1000000 INFO @ Tue, 02 Aug 2022 11:51:37: 2000000 INFO @ Tue, 02 Aug 2022 11:51:42: 3000000 INFO @ Tue, 02 Aug 2022 11:51:47: 4000000 INFO @ Tue, 02 Aug 2022 11:51:51: 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 11:51:56: 6000000 INFO @ Tue, 02 Aug 2022 11:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.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 11:51:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:51:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:01: 7000000 INFO @ Tue, 02 Aug 2022 11:52:02: 1000000 INFO @ Tue, 02 Aug 2022 11:52:06: 8000000 INFO @ Tue, 02 Aug 2022 11:52:07: 2000000 INFO @ Tue, 02 Aug 2022 11:52:11: 9000000 INFO @ Tue, 02 Aug 2022 11:52:12: 3000000 INFO @ Tue, 02 Aug 2022 11:52:16: 10000000 INFO @ Tue, 02 Aug 2022 11:52:17: 4000000 INFO @ Tue, 02 Aug 2022 11:52:21: 11000000 INFO @ Tue, 02 Aug 2022 11:52:22: 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 11:52:26: 12000000 INFO @ Tue, 02 Aug 2022 11:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.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 11:52:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:52:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:27: 6000000 INFO @ Tue, 02 Aug 2022 11:52:30: 13000000 INFO @ Tue, 02 Aug 2022 11:52:32: 1000000 INFO @ Tue, 02 Aug 2022 11:52:32: 7000000 INFO @ Tue, 02 Aug 2022 11:52:35: 14000000 INFO @ Tue, 02 Aug 2022 11:52:37: 2000000 INFO @ Tue, 02 Aug 2022 11:52:37: 8000000 INFO @ Tue, 02 Aug 2022 11:52:40: 15000000 INFO @ Tue, 02 Aug 2022 11:52:42: 3000000 INFO @ Tue, 02 Aug 2022 11:52:42: 9000000 INFO @ Tue, 02 Aug 2022 11:52:45: 16000000 INFO @ Tue, 02 Aug 2022 11:52:47: 10000000 INFO @ Tue, 02 Aug 2022 11:52:47: 4000000 INFO @ Tue, 02 Aug 2022 11:52:50: 17000000 INFO @ Tue, 02 Aug 2022 11:52:52: 11000000 INFO @ Tue, 02 Aug 2022 11:52:53: 5000000 INFO @ Tue, 02 Aug 2022 11:52:55: 18000000 INFO @ Tue, 02 Aug 2022 11:52:57: 12000000 INFO @ Tue, 02 Aug 2022 11:52:58: 6000000 INFO @ Tue, 02 Aug 2022 11:53:00: 19000000 INFO @ Tue, 02 Aug 2022 11:53:01: 13000000 INFO @ Tue, 02 Aug 2022 11:53:03: 7000000 INFO @ Tue, 02 Aug 2022 11:53:05: 20000000 INFO @ Tue, 02 Aug 2022 11:53:06: 14000000 INFO @ Tue, 02 Aug 2022 11:53:08: 8000000 INFO @ Tue, 02 Aug 2022 11:53:09: 21000000 INFO @ Tue, 02 Aug 2022 11:53:11: 15000000 INFO @ Tue, 02 Aug 2022 11:53:13: 9000000 INFO @ Tue, 02 Aug 2022 11:53:14: 22000000 INFO @ Tue, 02 Aug 2022 11:53:16: 16000000 INFO @ Tue, 02 Aug 2022 11:53:18: 10000000 INFO @ Tue, 02 Aug 2022 11:53:19: 23000000 INFO @ Tue, 02 Aug 2022 11:53:21: 17000000 INFO @ Tue, 02 Aug 2022 11:53:23: 11000000 INFO @ Tue, 02 Aug 2022 11:53:24: 24000000 INFO @ Tue, 02 Aug 2022 11:53:25: 18000000 INFO @ Tue, 02 Aug 2022 11:53:28: 12000000 INFO @ Tue, 02 Aug 2022 11:53:29: 25000000 INFO @ Tue, 02 Aug 2022 11:53:30: 19000000 INFO @ Tue, 02 Aug 2022 11:53:33: 13000000 INFO @ Tue, 02 Aug 2022 11:53:34: 26000000 INFO @ Tue, 02 Aug 2022 11:53:35: 20000000 INFO @ Tue, 02 Aug 2022 11:53:37: 14000000 INFO @ Tue, 02 Aug 2022 11:53:39: 27000000 INFO @ Tue, 02 Aug 2022 11:53:40: 21000000 INFO @ Tue, 02 Aug 2022 11:53:42: 15000000 INFO @ Tue, 02 Aug 2022 11:53:44: 28000000 INFO @ Tue, 02 Aug 2022 11:53:45: 22000000 INFO @ Tue, 02 Aug 2022 11:53:47: 16000000 INFO @ Tue, 02 Aug 2022 11:53:49: 29000000 INFO @ Tue, 02 Aug 2022 11:53:49: 23000000 INFO @ Tue, 02 Aug 2022 11:53:52: 17000000 INFO @ Tue, 02 Aug 2022 11:53:54: 30000000 INFO @ Tue, 02 Aug 2022 11:53:54: 24000000 INFO @ Tue, 02 Aug 2022 11:53:57: 18000000 INFO @ Tue, 02 Aug 2022 11:53:59: 31000000 INFO @ Tue, 02 Aug 2022 11:53:59: 25000000 INFO @ Tue, 02 Aug 2022 11:54:02: 19000000 INFO @ Tue, 02 Aug 2022 11:54:04: 26000000 INFO @ Tue, 02 Aug 2022 11:54:04: 32000000 INFO @ Tue, 02 Aug 2022 11:54:06: 20000000 INFO @ Tue, 02 Aug 2022 11:54:08: 27000000 INFO @ Tue, 02 Aug 2022 11:54:09: 33000000 INFO @ Tue, 02 Aug 2022 11:54:11: 21000000 INFO @ Tue, 02 Aug 2022 11:54:12: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:54:12: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:54:12: #1 total tags in treatment: 12880968 INFO @ Tue, 02 Aug 2022 11:54:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:54:12: #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 11:54:12: #1 tags after filtering in treatment: 9180824 INFO @ Tue, 02 Aug 2022 11:54:12: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 11:54:12: #1 finished! INFO @ Tue, 02 Aug 2022 11:54:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:54:13: #2 number of paired peaks: 3021 INFO @ Tue, 02 Aug 2022 11:54:13: start model_add_line... INFO @ Tue, 02 Aug 2022 11:54:13: start X-correlation... INFO @ Tue, 02 Aug 2022 11:54:13: 28000000 INFO @ Tue, 02 Aug 2022 11:54:13: end of X-cor INFO @ Tue, 02 Aug 2022 11:54:13: #2 finished! INFO @ Tue, 02 Aug 2022 11:54:13: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:54:13: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 11:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.05_model.r WARNING @ Tue, 02 Aug 2022 11:54:13: #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 11:54:13: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 11:54:13: #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 11:54:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:54:16: 22000000 INFO @ Tue, 02 Aug 2022 11:54:18: 29000000 INFO @ Tue, 02 Aug 2022 11:54:20: 23000000 INFO @ Tue, 02 Aug 2022 11:54:23: 30000000 INFO @ Tue, 02 Aug 2022 11:54:25: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:54:27: 31000000 INFO @ Tue, 02 Aug 2022 11:54:30: 25000000 INFO @ Tue, 02 Aug 2022 11:54:33: 32000000 INFO @ Tue, 02 Aug 2022 11:54:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:54:35: 26000000 INFO @ Tue, 02 Aug 2022 11:54:38: 33000000 INFO @ Tue, 02 Aug 2022 11:54:39: 27000000 INFO @ Tue, 02 Aug 2022 11:54:41: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:54:41: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:54:41: #1 total tags in treatment: 12880968 INFO @ Tue, 02 Aug 2022 11:54:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:54:41: #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 11:54:41: #1 tags after filtering in treatment: 9180824 INFO @ Tue, 02 Aug 2022 11:54:41: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 11:54:41: #1 finished! INFO @ Tue, 02 Aug 2022 11:54:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:54:42: #2 number of paired peaks: 3021 INFO @ Tue, 02 Aug 2022 11:54:42: start model_add_line... INFO @ Tue, 02 Aug 2022 11:54:42: start X-correlation... INFO @ Tue, 02 Aug 2022 11:54:42: end of X-cor INFO @ Tue, 02 Aug 2022 11:54:42: #2 finished! INFO @ Tue, 02 Aug 2022 11:54:42: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:54:42: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 11:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.10_model.r WARNING @ Tue, 02 Aug 2022 11:54:42: #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 11:54:42: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 11:54:42: #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 11:54:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:54:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.05_summits.bed INFO @ Tue, 02 Aug 2022 11:54:43: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16271 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:54:44: 28000000 INFO @ Tue, 02 Aug 2022 11:54:49: 29000000 INFO @ Tue, 02 Aug 2022 11:54:53: 30000000 INFO @ Tue, 02 Aug 2022 11:54:57: 31000000 INFO @ Tue, 02 Aug 2022 11:55:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:55:02: 32000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:55:06: 33000000 INFO @ Tue, 02 Aug 2022 11:55:09: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:55:09: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:55:09: #1 total tags in treatment: 12880968 INFO @ Tue, 02 Aug 2022 11:55:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:55:09: #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 11:55:09: #1 tags after filtering in treatment: 9180824 INFO @ Tue, 02 Aug 2022 11:55:09: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 11:55:09: #1 finished! INFO @ Tue, 02 Aug 2022 11:55:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:55:10: #2 number of paired peaks: 3021 INFO @ Tue, 02 Aug 2022 11:55:10: start model_add_line... INFO @ Tue, 02 Aug 2022 11:55:10: start X-correlation... INFO @ Tue, 02 Aug 2022 11:55:10: end of X-cor INFO @ Tue, 02 Aug 2022 11:55:10: #2 finished! INFO @ Tue, 02 Aug 2022 11:55:10: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 11:55:10: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 11:55:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.20_model.r WARNING @ Tue, 02 Aug 2022 11:55:10: #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 11:55:10: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 11:55:10: #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 11:55:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.10_summits.bed INFO @ Tue, 02 Aug 2022 11:55:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8330 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:55:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178852/SRX12178852.20_summits.bed INFO @ Tue, 02 Aug 2022 11:55:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1557 records, 4 fields): 24 millis CompletedMACS2peakCalling