Job ID = 16436203 SRX = SRX12178854 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:05:30 prefetch.2.10.7: 1) Downloading 'SRR15888060'... 2022-08-02T02:05:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:09:00 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:09:00 prefetch.2.10.7: 1) 'SRR15888060' was downloaded successfully 2022-08-02T02:09:00 prefetch.2.10.7: 'SRR15888060' has 0 unresolved dependencies Read 39996336 spots for SRR15888060/SRR15888060.sra Written 39996336 spots for SRR15888060/SRR15888060.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436805 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:30:38 39996336 reads; of these: 39996336 (100.00%) were paired; of these: 17691612 (44.23%) aligned concordantly 0 times 19576773 (48.95%) aligned concordantly exactly 1 time 2727951 (6.82%) aligned concordantly >1 times ---- 17691612 pairs aligned concordantly 0 times; of these: 3759726 (21.25%) aligned discordantly 1 time ---- 13931886 pairs aligned 0 times concordantly or discordantly; of these: 27863772 mates make up the pairs; of these: 23444833 (84.14%) aligned 0 times 3316730 (11.90%) aligned exactly 1 time 1102209 (3.96%) aligned >1 times 70.69% overall alignment rate Time searching: 00:30:39 Overall time: 00:30:39 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] 10980824 / 25982880 = 0.4226 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 11:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.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 11:55:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:55:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:55:31: 1000000 INFO @ Tue, 02 Aug 2022 11:55:37: 2000000 INFO @ Tue, 02 Aug 2022 11:55:43: 3000000 INFO @ Tue, 02 Aug 2022 11:55:48: 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 11:55:54: 5000000 INFO @ Tue, 02 Aug 2022 11:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.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 11:55:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:55:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:56:00: 6000000 INFO @ Tue, 02 Aug 2022 11:56:01: 1000000 INFO @ Tue, 02 Aug 2022 11:56:07: 7000000 INFO @ Tue, 02 Aug 2022 11:56:08: 2000000 INFO @ Tue, 02 Aug 2022 11:56:13: 8000000 INFO @ Tue, 02 Aug 2022 11:56:15: 3000000 INFO @ Tue, 02 Aug 2022 11:56:20: 9000000 INFO @ Tue, 02 Aug 2022 11:56:22: 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 11:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.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 11:56:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:56:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:56:27: 10000000 INFO @ Tue, 02 Aug 2022 11:56:28: 5000000 INFO @ Tue, 02 Aug 2022 11:56:31: 1000000 INFO @ Tue, 02 Aug 2022 11:56:33: 11000000 INFO @ Tue, 02 Aug 2022 11:56:35: 6000000 INFO @ Tue, 02 Aug 2022 11:56:38: 2000000 INFO @ Tue, 02 Aug 2022 11:56:40: 12000000 INFO @ Tue, 02 Aug 2022 11:56:41: 7000000 INFO @ Tue, 02 Aug 2022 11:56:45: 3000000 INFO @ Tue, 02 Aug 2022 11:56:46: 13000000 INFO @ Tue, 02 Aug 2022 11:56:47: 8000000 INFO @ Tue, 02 Aug 2022 11:56:51: 4000000 INFO @ Tue, 02 Aug 2022 11:56:53: 14000000 INFO @ Tue, 02 Aug 2022 11:56:54: 9000000 INFO @ Tue, 02 Aug 2022 11:56:57: 5000000 INFO @ Tue, 02 Aug 2022 11:56:59: 15000000 INFO @ Tue, 02 Aug 2022 11:57:00: 10000000 INFO @ Tue, 02 Aug 2022 11:57:04: 6000000 INFO @ Tue, 02 Aug 2022 11:57:06: 16000000 INFO @ Tue, 02 Aug 2022 11:57:06: 11000000 INFO @ Tue, 02 Aug 2022 11:57:10: 7000000 INFO @ Tue, 02 Aug 2022 11:57:12: 17000000 INFO @ Tue, 02 Aug 2022 11:57:13: 12000000 INFO @ Tue, 02 Aug 2022 11:57:17: 8000000 INFO @ Tue, 02 Aug 2022 11:57:19: 18000000 INFO @ Tue, 02 Aug 2022 11:57:19: 13000000 INFO @ Tue, 02 Aug 2022 11:57:23: 9000000 INFO @ Tue, 02 Aug 2022 11:57:25: 19000000 INFO @ Tue, 02 Aug 2022 11:57:25: 14000000 INFO @ Tue, 02 Aug 2022 11:57:30: 10000000 INFO @ Tue, 02 Aug 2022 11:57:31: 20000000 INFO @ Tue, 02 Aug 2022 11:57:32: 15000000 INFO @ Tue, 02 Aug 2022 11:57:36: 11000000 INFO @ Tue, 02 Aug 2022 11:57:37: 21000000 INFO @ Tue, 02 Aug 2022 11:57:38: 16000000 INFO @ Tue, 02 Aug 2022 11:57:42: 12000000 INFO @ Tue, 02 Aug 2022 11:57:44: 22000000 INFO @ Tue, 02 Aug 2022 11:57:44: 17000000 INFO @ Tue, 02 Aug 2022 11:57:48: 13000000 INFO @ Tue, 02 Aug 2022 11:57:50: 23000000 INFO @ Tue, 02 Aug 2022 11:57:50: 18000000 INFO @ Tue, 02 Aug 2022 11:57:55: 14000000 INFO @ Tue, 02 Aug 2022 11:57:56: 24000000 INFO @ Tue, 02 Aug 2022 11:57:56: 19000000 INFO @ Tue, 02 Aug 2022 11:58:01: 15000000 INFO @ Tue, 02 Aug 2022 11:58:02: 25000000 INFO @ Tue, 02 Aug 2022 11:58:03: 20000000 INFO @ Tue, 02 Aug 2022 11:58:07: 16000000 INFO @ Tue, 02 Aug 2022 11:58:08: 26000000 INFO @ Tue, 02 Aug 2022 11:58:09: 21000000 INFO @ Tue, 02 Aug 2022 11:58:13: 17000000 INFO @ Tue, 02 Aug 2022 11:58:14: 27000000 INFO @ Tue, 02 Aug 2022 11:58:15: 22000000 INFO @ Tue, 02 Aug 2022 11:58:20: 18000000 INFO @ Tue, 02 Aug 2022 11:58:21: 28000000 INFO @ Tue, 02 Aug 2022 11:58:21: 23000000 INFO @ Tue, 02 Aug 2022 11:58:26: 19000000 INFO @ Tue, 02 Aug 2022 11:58:27: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:58:27: 24000000 INFO @ Tue, 02 Aug 2022 11:58:32: 20000000 INFO @ Tue, 02 Aug 2022 11:58:33: 30000000 INFO @ Tue, 02 Aug 2022 11:58:33: 25000000 INFO @ Tue, 02 Aug 2022 11:58:38: 21000000 INFO @ Tue, 02 Aug 2022 11:58:39: 31000000 INFO @ Tue, 02 Aug 2022 11:58:40: 26000000 INFO @ Tue, 02 Aug 2022 11:58:45: 22000000 INFO @ Tue, 02 Aug 2022 11:58:46: 32000000 INFO @ Tue, 02 Aug 2022 11:58:46: 27000000 INFO @ Tue, 02 Aug 2022 11:58:51: 23000000 INFO @ Tue, 02 Aug 2022 11:58:52: 33000000 INFO @ Tue, 02 Aug 2022 11:58:52: 28000000 INFO @ Tue, 02 Aug 2022 11:58:57: 24000000 INFO @ Tue, 02 Aug 2022 11:58:58: 34000000 INFO @ Tue, 02 Aug 2022 11:58:59: 29000000 INFO @ Tue, 02 Aug 2022 11:59:02: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:59:02: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:59:02: #1 total tags in treatment: 12588566 INFO @ Tue, 02 Aug 2022 11:59:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:02: #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 11:59:03: #1 tags after filtering in treatment: 9057173 INFO @ Tue, 02 Aug 2022 11:59:03: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 11:59:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:03: #2 number of paired peaks: 2991 INFO @ Tue, 02 Aug 2022 11:59:03: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:03: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:04: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 11:59:04: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 11:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.05_model.r INFO @ Tue, 02 Aug 2022 11:59:04: 25000000 WARNING @ Tue, 02 Aug 2022 11:59:04: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:59:04: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 11:59:04: #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 11:59:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:05: 30000000 INFO @ Tue, 02 Aug 2022 11:59:10: 26000000 INFO @ Tue, 02 Aug 2022 11:59:11: 31000000 INFO @ Tue, 02 Aug 2022 11:59:16: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:59:17: 32000000 INFO @ Tue, 02 Aug 2022 11:59:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:22: 28000000 INFO @ Tue, 02 Aug 2022 11:59:23: 33000000 INFO @ Tue, 02 Aug 2022 11:59:28: 29000000 INFO @ Tue, 02 Aug 2022 11:59:29: 34000000 INFO @ Tue, 02 Aug 2022 11:59:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:59:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.05_summits.bed INFO @ Tue, 02 Aug 2022 11:59:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (17189 records, 4 fields): 127 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:59:33: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:59:33: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:59:33: #1 total tags in treatment: 12588566 INFO @ Tue, 02 Aug 2022 11:59:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:33: #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 11:59:33: #1 tags after filtering in treatment: 9057173 INFO @ Tue, 02 Aug 2022 11:59:33: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 11:59:33: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:34: #2 number of paired peaks: 2991 INFO @ Tue, 02 Aug 2022 11:59:34: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:34: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:34: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:34: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:34: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 11:59:34: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 11:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.10_model.r WARNING @ Tue, 02 Aug 2022 11:59:34: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:59:34: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 11:59:34: #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 11:59:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:36: 30000000 INFO @ Tue, 02 Aug 2022 11:59:41: 31000000 INFO @ Tue, 02 Aug 2022 11:59:47: 32000000 INFO @ Tue, 02 Aug 2022 11:59:52: 33000000 INFO @ Tue, 02 Aug 2022 11:59:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:00:00: 34000000 INFO @ Tue, 02 Aug 2022 12:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.10_summits.bed INFO @ Tue, 02 Aug 2022 12:00:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9028 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:00:03: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:00:03: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:00:03: #1 total tags in treatment: 12588566 INFO @ Tue, 02 Aug 2022 12:00:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:00:03: #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 12:00:03: #1 tags after filtering in treatment: 9057173 INFO @ Tue, 02 Aug 2022 12:00:03: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 12:00:03: #1 finished! INFO @ Tue, 02 Aug 2022 12:00:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:00:04: #2 number of paired peaks: 2991 INFO @ Tue, 02 Aug 2022 12:00:04: start model_add_line... INFO @ Tue, 02 Aug 2022 12:00:04: start X-correlation... INFO @ Tue, 02 Aug 2022 12:00:04: end of X-cor INFO @ Tue, 02 Aug 2022 12:00:04: #2 finished! INFO @ Tue, 02 Aug 2022 12:00:04: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 12:00:04: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 12:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.20_model.r WARNING @ Tue, 02 Aug 2022 12:00:04: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:00:04: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 12:00:04: #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 12:00:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:00:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178854/SRX12178854.20_summits.bed INFO @ Tue, 02 Aug 2022 12:00:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1770 records, 4 fields): 93 millis CompletedMACS2peakCalling