Job ID = 16436232 SRX = SRX12178876 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:10:22 prefetch.2.10.7: 1) Downloading 'SRR15888038'... 2022-08-02T02:10:22 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:12:31 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:12:31 prefetch.2.10.7: 1) 'SRR15888038' was downloaded successfully 2022-08-02T02:12:31 prefetch.2.10.7: 'SRR15888038' has 0 unresolved dependencies Read 40535566 spots for SRR15888038/SRR15888038.sra Written 40535566 spots for SRR15888038/SRR15888038.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436826 ("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: 00:34:24 40535566 reads; of these: 40535566 (100.00%) were paired; of these: 17392122 (42.91%) aligned concordantly 0 times 20250984 (49.96%) aligned concordantly exactly 1 time 2892460 (7.14%) aligned concordantly >1 times ---- 17392122 pairs aligned concordantly 0 times; of these: 3745703 (21.54%) aligned discordantly 1 time ---- 13646419 pairs aligned 0 times concordantly or discordantly; of these: 27292838 mates make up the pairs; of these: 23474845 (86.01%) aligned 0 times 2796248 (10.25%) aligned exactly 1 time 1021745 (3.74%) aligned >1 times 71.04% overall alignment rate Time searching: 00:34:24 Overall time: 00:34:24 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] 10428062 / 26760423 = 0.3897 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 12:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.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 12:02:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:02:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:02:23: 1000000 INFO @ Tue, 02 Aug 2022 12:02:29: 2000000 INFO @ Tue, 02 Aug 2022 12:02:36: 3000000 INFO @ Tue, 02 Aug 2022 12:02:42: 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 12:02:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.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 12:02:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:02:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:02:49: 5000000 INFO @ Tue, 02 Aug 2022 12:02:53: 1000000 INFO @ Tue, 02 Aug 2022 12:02:56: 6000000 INFO @ Tue, 02 Aug 2022 12:03:01: 2000000 INFO @ Tue, 02 Aug 2022 12:03:04: 7000000 INFO @ Tue, 02 Aug 2022 12:03:08: 3000000 INFO @ Tue, 02 Aug 2022 12:03:11: 8000000 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 12:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.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 12:03:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:03:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:03:16: 4000000 INFO @ Tue, 02 Aug 2022 12:03:19: 9000000 INFO @ Tue, 02 Aug 2022 12:03:24: 5000000 INFO @ Tue, 02 Aug 2022 12:03:24: 1000000 INFO @ Tue, 02 Aug 2022 12:03:27: 10000000 INFO @ Tue, 02 Aug 2022 12:03:32: 6000000 INFO @ Tue, 02 Aug 2022 12:03:32: 2000000 INFO @ Tue, 02 Aug 2022 12:03:35: 11000000 INFO @ Tue, 02 Aug 2022 12:03:39: 7000000 INFO @ Tue, 02 Aug 2022 12:03:40: 3000000 INFO @ Tue, 02 Aug 2022 12:03:43: 12000000 INFO @ Tue, 02 Aug 2022 12:03:47: 8000000 INFO @ Tue, 02 Aug 2022 12:03:48: 4000000 INFO @ Tue, 02 Aug 2022 12:03:51: 13000000 INFO @ Tue, 02 Aug 2022 12:03:55: 9000000 INFO @ Tue, 02 Aug 2022 12:03:55: 5000000 INFO @ Tue, 02 Aug 2022 12:03:59: 14000000 INFO @ Tue, 02 Aug 2022 12:04:02: 10000000 INFO @ Tue, 02 Aug 2022 12:04:03: 6000000 INFO @ Tue, 02 Aug 2022 12:04:06: 15000000 INFO @ Tue, 02 Aug 2022 12:04:10: 11000000 INFO @ Tue, 02 Aug 2022 12:04:11: 7000000 INFO @ Tue, 02 Aug 2022 12:04:14: 16000000 INFO @ Tue, 02 Aug 2022 12:04:17: 12000000 INFO @ Tue, 02 Aug 2022 12:04:18: 8000000 INFO @ Tue, 02 Aug 2022 12:04:22: 17000000 INFO @ Tue, 02 Aug 2022 12:04:25: 13000000 INFO @ Tue, 02 Aug 2022 12:04:26: 9000000 INFO @ Tue, 02 Aug 2022 12:04:30: 18000000 INFO @ Tue, 02 Aug 2022 12:04:33: 14000000 INFO @ Tue, 02 Aug 2022 12:04:33: 10000000 INFO @ Tue, 02 Aug 2022 12:04:37: 19000000 INFO @ Tue, 02 Aug 2022 12:04:40: 15000000 INFO @ Tue, 02 Aug 2022 12:04:41: 11000000 INFO @ Tue, 02 Aug 2022 12:04:45: 20000000 INFO @ Tue, 02 Aug 2022 12:04:48: 16000000 INFO @ Tue, 02 Aug 2022 12:04:48: 12000000 INFO @ Tue, 02 Aug 2022 12:04:53: 21000000 INFO @ Tue, 02 Aug 2022 12:04:56: 17000000 INFO @ Tue, 02 Aug 2022 12:04:56: 13000000 INFO @ Tue, 02 Aug 2022 12:05:00: 22000000 INFO @ Tue, 02 Aug 2022 12:05:03: 18000000 INFO @ Tue, 02 Aug 2022 12:05:03: 14000000 INFO @ Tue, 02 Aug 2022 12:05:07: 23000000 INFO @ Tue, 02 Aug 2022 12:05:11: 19000000 INFO @ Tue, 02 Aug 2022 12:05:11: 15000000 INFO @ Tue, 02 Aug 2022 12:05:15: 24000000 INFO @ Tue, 02 Aug 2022 12:05:18: 16000000 INFO @ Tue, 02 Aug 2022 12:05:18: 20000000 INFO @ Tue, 02 Aug 2022 12:05:23: 25000000 INFO @ Tue, 02 Aug 2022 12:05:26: 21000000 INFO @ Tue, 02 Aug 2022 12:05:26: 17000000 INFO @ Tue, 02 Aug 2022 12:05:30: 26000000 INFO @ Tue, 02 Aug 2022 12:05:33: 22000000 INFO @ Tue, 02 Aug 2022 12:05:33: 18000000 INFO @ Tue, 02 Aug 2022 12:05:37: 27000000 INFO @ Tue, 02 Aug 2022 12:05:40: 23000000 INFO @ Tue, 02 Aug 2022 12:05:40: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:05:45: 28000000 INFO @ Tue, 02 Aug 2022 12:05:47: 24000000 INFO @ Tue, 02 Aug 2022 12:05:48: 20000000 INFO @ Tue, 02 Aug 2022 12:05:52: 29000000 INFO @ Tue, 02 Aug 2022 12:05:54: 25000000 INFO @ Tue, 02 Aug 2022 12:05:55: 21000000 INFO @ Tue, 02 Aug 2022 12:05:59: 30000000 INFO @ Tue, 02 Aug 2022 12:06:02: 26000000 INFO @ Tue, 02 Aug 2022 12:06:03: 22000000 INFO @ Tue, 02 Aug 2022 12:06:07: 31000000 INFO @ Tue, 02 Aug 2022 12:06:10: 27000000 INFO @ Tue, 02 Aug 2022 12:06:10: 23000000 INFO @ Tue, 02 Aug 2022 12:06:14: 32000000 INFO @ Tue, 02 Aug 2022 12:06:18: 28000000 INFO @ Tue, 02 Aug 2022 12:06:18: 24000000 INFO @ Tue, 02 Aug 2022 12:06:22: 33000000 INFO @ Tue, 02 Aug 2022 12:06:25: 25000000 INFO @ Tue, 02 Aug 2022 12:06:25: 29000000 INFO @ Tue, 02 Aug 2022 12:06:29: 34000000 INFO @ Tue, 02 Aug 2022 12:06:33: 26000000 INFO @ Tue, 02 Aug 2022 12:06:33: 30000000 INFO @ Tue, 02 Aug 2022 12:06:37: 35000000 INFO @ Tue, 02 Aug 2022 12:06:40: 27000000 INFO @ Tue, 02 Aug 2022 12:06:41: 31000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:06:44: 36000000 INFO @ Tue, 02 Aug 2022 12:06:47: 28000000 INFO @ Tue, 02 Aug 2022 12:06:48: 32000000 INFO @ Tue, 02 Aug 2022 12:06:49: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:06:49: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:06:49: #1 total tags in treatment: 13994760 INFO @ Tue, 02 Aug 2022 12:06:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:06:49: #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 12:06:49: #1 tags after filtering in treatment: 10737107 INFO @ Tue, 02 Aug 2022 12:06:49: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 12:06:49: #1 finished! INFO @ Tue, 02 Aug 2022 12:06:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:06:50: #2 number of paired peaks: 1158 INFO @ Tue, 02 Aug 2022 12:06:50: start model_add_line... INFO @ Tue, 02 Aug 2022 12:06:50: start X-correlation... INFO @ Tue, 02 Aug 2022 12:06:50: end of X-cor INFO @ Tue, 02 Aug 2022 12:06:50: #2 finished! INFO @ Tue, 02 Aug 2022 12:06:50: #2 predicted fragment length is 14 bps INFO @ Tue, 02 Aug 2022 12:06:50: #2 alternative fragment length(s) may be 4,14,28,48 bps INFO @ Tue, 02 Aug 2022 12:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.05_model.r WARNING @ Tue, 02 Aug 2022 12:06:50: #2 Since the d (14) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:06:50: #2 You may need to consider one of the other alternative d(s): 4,14,28,48 WARNING @ Tue, 02 Aug 2022 12:06:50: #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 12:06:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:06:55: 29000000 INFO @ Tue, 02 Aug 2022 12:06:56: 33000000 INFO @ Tue, 02 Aug 2022 12:07:02: 30000000 INFO @ Tue, 02 Aug 2022 12:07:03: 34000000 INFO @ Tue, 02 Aug 2022 12:07:09: 31000000 INFO @ Tue, 02 Aug 2022 12:07:10: 35000000 INFO @ Tue, 02 Aug 2022 12:07:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:07:16: 32000000 INFO @ Tue, 02 Aug 2022 12:07:18: 36000000 INFO @ Tue, 02 Aug 2022 12:07:23: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:07:23: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:07:23: #1 total tags in treatment: 13994760 INFO @ Tue, 02 Aug 2022 12:07:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:07:23: #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 12:07:23: #1 tags after filtering in treatment: 10737107 INFO @ Tue, 02 Aug 2022 12:07:23: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 12:07:23: #1 finished! INFO @ Tue, 02 Aug 2022 12:07:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:07:23: 33000000 INFO @ Tue, 02 Aug 2022 12:07:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:07:24: #2 number of paired peaks: 1158 INFO @ Tue, 02 Aug 2022 12:07:24: start model_add_line... INFO @ Tue, 02 Aug 2022 12:07:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:07:24: start X-correlation... INFO @ Tue, 02 Aug 2022 12:07:24: end of X-cor INFO @ Tue, 02 Aug 2022 12:07:24: #2 finished! INFO @ Tue, 02 Aug 2022 12:07:24: #2 predicted fragment length is 14 bps INFO @ Tue, 02 Aug 2022 12:07:24: #2 alternative fragment length(s) may be 4,14,28,48 bps INFO @ Tue, 02 Aug 2022 12:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.10_model.r WARNING @ Tue, 02 Aug 2022 12:07:24: #2 Since the d (14) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:07:24: #2 You may need to consider one of the other alternative d(s): 4,14,28,48 WARNING @ Tue, 02 Aug 2022 12:07:24: #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 12:07:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:07:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.05_summits.bed INFO @ Tue, 02 Aug 2022 12:07:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (8417 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:07:30: 34000000 INFO @ Tue, 02 Aug 2022 12:07:36: 35000000 INFO @ Tue, 02 Aug 2022 12:07:42: 36000000 INFO @ Tue, 02 Aug 2022 12:07:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:07:46: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:07:46: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:07:46: #1 total tags in treatment: 13994760 INFO @ Tue, 02 Aug 2022 12:07:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:07:46: #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 12:07:46: #1 tags after filtering in treatment: 10737107 INFO @ Tue, 02 Aug 2022 12:07:46: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 12:07:46: #1 finished! INFO @ Tue, 02 Aug 2022 12:07:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:07:47: #2 number of paired peaks: 1158 INFO @ Tue, 02 Aug 2022 12:07:47: start model_add_line... INFO @ Tue, 02 Aug 2022 12:07:47: start X-correlation... INFO @ Tue, 02 Aug 2022 12:07:47: end of X-cor INFO @ Tue, 02 Aug 2022 12:07:47: #2 finished! INFO @ Tue, 02 Aug 2022 12:07:47: #2 predicted fragment length is 14 bps INFO @ Tue, 02 Aug 2022 12:07:47: #2 alternative fragment length(s) may be 4,14,28,48 bps INFO @ Tue, 02 Aug 2022 12:07:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.20_model.r WARNING @ Tue, 02 Aug 2022 12:07:47: #2 Since the d (14) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:07:47: #2 You may need to consider one of the other alternative d(s): 4,14,28,48 WARNING @ Tue, 02 Aug 2022 12:07:47: #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 12:07:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:07:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:07:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:07:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:07:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.10_summits.bed INFO @ Tue, 02 Aug 2022 12:07:56: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:08:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178876/SRX12178876.20_summits.bed INFO @ Tue, 02 Aug 2022 12:08:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling