Job ID = 16436205 SRX = SRX12178856 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:05:43 prefetch.2.10.7: 1) Downloading 'SRR15888058'... 2022-08-02T02:05:43 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:08:29 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:08:29 prefetch.2.10.7: 1) 'SRR15888058' was downloaded successfully 2022-08-02T02:08:29 prefetch.2.10.7: 'SRR15888058' has 0 unresolved dependencies Read 60216519 spots for SRR15888058/SRR15888058.sra Written 60216519 spots for SRR15888058/SRR15888058.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436813 ("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: 00:28:47 60216519 reads; of these: 60216519 (100.00%) were paired; of these: 41677120 (69.21%) aligned concordantly 0 times 15654948 (26.00%) aligned concordantly exactly 1 time 2884451 (4.79%) aligned concordantly >1 times ---- 41677120 pairs aligned concordantly 0 times; of these: 3200020 (7.68%) aligned discordantly 1 time ---- 38477100 pairs aligned 0 times concordantly or discordantly; of these: 76954200 mates make up the pairs; of these: 73386764 (95.36%) aligned 0 times 2516276 (3.27%) aligned exactly 1 time 1051160 (1.37%) aligned >1 times 39.06% overall alignment rate Time searching: 00:28:47 Overall time: 00:28:47 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] 7691165 / 21606401 = 0.3560 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 11:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.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 11:55:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:55:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:55:46: 1000000 INFO @ Tue, 02 Aug 2022 11:55:51: 2000000 INFO @ Tue, 02 Aug 2022 11:55:55: 3000000 INFO @ Tue, 02 Aug 2022 11:55:59: 4000000 INFO @ Tue, 02 Aug 2022 11:56:04: 5000000 INFO @ Tue, 02 Aug 2022 11:56:08: 6000000 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 11:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.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 11:56:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:56:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:56:12: 7000000 INFO @ Tue, 02 Aug 2022 11:56:16: 1000000 INFO @ Tue, 02 Aug 2022 11:56:17: 8000000 INFO @ Tue, 02 Aug 2022 11:56:20: 2000000 INFO @ Tue, 02 Aug 2022 11:56:21: 9000000 INFO @ Tue, 02 Aug 2022 11:56:25: 3000000 INFO @ Tue, 02 Aug 2022 11:56:26: 10000000 INFO @ Tue, 02 Aug 2022 11:56:30: 4000000 INFO @ Tue, 02 Aug 2022 11:56:30: 11000000 INFO @ Tue, 02 Aug 2022 11:56:34: 5000000 INFO @ Tue, 02 Aug 2022 11:56:34: 12000000 INFO @ Tue, 02 Aug 2022 11:56:39: 6000000 INFO @ Tue, 02 Aug 2022 11:56:39: 13000000 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 11:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.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 11:56:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:56:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:56:43: 7000000 INFO @ Tue, 02 Aug 2022 11:56:43: 14000000 INFO @ Tue, 02 Aug 2022 11:56:46: 1000000 INFO @ Tue, 02 Aug 2022 11:56:48: 15000000 INFO @ Tue, 02 Aug 2022 11:56:48: 8000000 INFO @ Tue, 02 Aug 2022 11:56:50: 2000000 INFO @ Tue, 02 Aug 2022 11:56:52: 16000000 INFO @ Tue, 02 Aug 2022 11:56:52: 9000000 INFO @ Tue, 02 Aug 2022 11:56:55: 3000000 INFO @ Tue, 02 Aug 2022 11:56:56: 17000000 INFO @ Tue, 02 Aug 2022 11:56:57: 10000000 INFO @ Tue, 02 Aug 2022 11:56:59: 4000000 INFO @ Tue, 02 Aug 2022 11:57:01: 18000000 INFO @ Tue, 02 Aug 2022 11:57:01: 11000000 INFO @ Tue, 02 Aug 2022 11:57:04: 5000000 INFO @ Tue, 02 Aug 2022 11:57:05: 19000000 INFO @ Tue, 02 Aug 2022 11:57:06: 12000000 INFO @ Tue, 02 Aug 2022 11:57:09: 6000000 INFO @ Tue, 02 Aug 2022 11:57:09: 20000000 INFO @ Tue, 02 Aug 2022 11:57:10: 13000000 INFO @ Tue, 02 Aug 2022 11:57:13: 7000000 INFO @ Tue, 02 Aug 2022 11:57:14: 21000000 INFO @ Tue, 02 Aug 2022 11:57:15: 14000000 INFO @ Tue, 02 Aug 2022 11:57:18: 8000000 INFO @ Tue, 02 Aug 2022 11:57:18: 22000000 INFO @ Tue, 02 Aug 2022 11:57:19: 15000000 INFO @ Tue, 02 Aug 2022 11:57:22: 9000000 INFO @ Tue, 02 Aug 2022 11:57:22: 23000000 INFO @ Tue, 02 Aug 2022 11:57:23: 16000000 INFO @ Tue, 02 Aug 2022 11:57:27: 10000000 INFO @ Tue, 02 Aug 2022 11:57:27: 24000000 INFO @ Tue, 02 Aug 2022 11:57:28: 17000000 INFO @ Tue, 02 Aug 2022 11:57:31: 11000000 INFO @ Tue, 02 Aug 2022 11:57:31: 25000000 INFO @ Tue, 02 Aug 2022 11:57:32: 18000000 INFO @ Tue, 02 Aug 2022 11:57:35: 12000000 INFO @ Tue, 02 Aug 2022 11:57:35: 26000000 INFO @ Tue, 02 Aug 2022 11:57:37: 19000000 INFO @ Tue, 02 Aug 2022 11:57:40: 13000000 INFO @ Tue, 02 Aug 2022 11:57:40: 27000000 INFO @ Tue, 02 Aug 2022 11:57:41: 20000000 INFO @ Tue, 02 Aug 2022 11:57:44: 14000000 INFO @ Tue, 02 Aug 2022 11:57:44: 28000000 INFO @ Tue, 02 Aug 2022 11:57:45: 21000000 INFO @ Tue, 02 Aug 2022 11:57:48: 15000000 INFO @ Tue, 02 Aug 2022 11:57:48: 29000000 INFO @ Tue, 02 Aug 2022 11:57:50: 22000000 INFO @ Tue, 02 Aug 2022 11:57:53: 30000000 INFO @ Tue, 02 Aug 2022 11:57:53: 16000000 INFO @ Tue, 02 Aug 2022 11:57:54: 23000000 INFO @ Tue, 02 Aug 2022 11:57:57: 31000000 INFO @ Tue, 02 Aug 2022 11:57:57: 17000000 INFO @ Tue, 02 Aug 2022 11:57:59: 24000000 INFO @ Tue, 02 Aug 2022 11:58:00: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:58:00: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:58:00: #1 total tags in treatment: 11899463 INFO @ Tue, 02 Aug 2022 11:58:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:58:00: #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 11:58:00: #1 tags after filtering in treatment: 9512366 INFO @ Tue, 02 Aug 2022 11:58:00: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 11:58:00: #1 finished! INFO @ Tue, 02 Aug 2022 11:58:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:58:01: #2 number of paired peaks: 777 WARNING @ Tue, 02 Aug 2022 11:58:01: Fewer paired peaks (777) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 777 pairs to build model! INFO @ Tue, 02 Aug 2022 11:58:01: start model_add_line... INFO @ Tue, 02 Aug 2022 11:58:01: start X-correlation... INFO @ Tue, 02 Aug 2022 11:58:01: end of X-cor INFO @ Tue, 02 Aug 2022 11:58:01: #2 finished! INFO @ Tue, 02 Aug 2022 11:58:01: #2 predicted fragment length is 12 bps INFO @ Tue, 02 Aug 2022 11:58:01: #2 alternative fragment length(s) may be 4,12,41 bps INFO @ Tue, 02 Aug 2022 11:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.05_model.r WARNING @ Tue, 02 Aug 2022 11:58:01: #2 Since the d (12) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:58:01: #2 You may need to consider one of the other alternative d(s): 4,12,41 WARNING @ Tue, 02 Aug 2022 11:58:01: #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 11:58:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:58:01: 18000000 INFO @ Tue, 02 Aug 2022 11:58:03: 25000000 INFO @ Tue, 02 Aug 2022 11:58:06: 19000000 INFO @ Tue, 02 Aug 2022 11:58:07: 26000000 INFO @ Tue, 02 Aug 2022 11:58:10: 20000000 INFO @ Tue, 02 Aug 2022 11:58:12: 27000000 INFO @ Tue, 02 Aug 2022 11:58:15: 21000000 INFO @ Tue, 02 Aug 2022 11:58:16: 28000000 INFO @ Tue, 02 Aug 2022 11:58:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:19: 22000000 INFO @ Tue, 02 Aug 2022 11:58:21: 29000000 INFO @ Tue, 02 Aug 2022 11:58:23: 23000000 INFO @ Tue, 02 Aug 2022 11:58:25: 30000000 INFO @ Tue, 02 Aug 2022 11:58:28: 24000000 INFO @ Tue, 02 Aug 2022 11:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.05_summits.bed INFO @ Tue, 02 Aug 2022 11:58:29: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2659 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:58:30: 31000000 INFO @ Tue, 02 Aug 2022 11:58:32: 25000000 INFO @ Tue, 02 Aug 2022 11:58:33: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:58:33: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:58:33: #1 total tags in treatment: 11899463 INFO @ Tue, 02 Aug 2022 11:58:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:58:33: #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 11:58:33: #1 tags after filtering in treatment: 9512366 INFO @ Tue, 02 Aug 2022 11:58:33: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 11:58:33: #1 finished! INFO @ Tue, 02 Aug 2022 11:58:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:58:34: #2 number of paired peaks: 777 WARNING @ Tue, 02 Aug 2022 11:58:34: Fewer paired peaks (777) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 777 pairs to build model! INFO @ Tue, 02 Aug 2022 11:58:34: start model_add_line... INFO @ Tue, 02 Aug 2022 11:58:34: start X-correlation... INFO @ Tue, 02 Aug 2022 11:58:34: end of X-cor INFO @ Tue, 02 Aug 2022 11:58:34: #2 finished! INFO @ Tue, 02 Aug 2022 11:58:34: #2 predicted fragment length is 12 bps INFO @ Tue, 02 Aug 2022 11:58:34: #2 alternative fragment length(s) may be 4,12,41 bps INFO @ Tue, 02 Aug 2022 11:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.10_model.r WARNING @ Tue, 02 Aug 2022 11:58:34: #2 Since the d (12) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:58:34: #2 You may need to consider one of the other alternative d(s): 4,12,41 WARNING @ Tue, 02 Aug 2022 11:58:34: #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 11:58:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:58:37: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:58:41: 27000000 INFO @ Tue, 02 Aug 2022 11:58:45: 28000000 INFO @ Tue, 02 Aug 2022 11:58:50: 29000000 INFO @ Tue, 02 Aug 2022 11:58:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:54: 30000000 INFO @ Tue, 02 Aug 2022 11:58:58: 31000000 INFO @ Tue, 02 Aug 2022 11:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.10_summits.bed INFO @ Tue, 02 Aug 2022 11:59:01: Done! INFO @ Tue, 02 Aug 2022 11:59:01: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:59:01: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:59:01: #1 total tags in treatment: 11899463 INFO @ Tue, 02 Aug 2022 11:59:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:59:02: #1 tags after filtering in treatment: 9512366 INFO @ Tue, 02 Aug 2022 11:59:02: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 11:59:02: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:02: #2 number of paired peaks: 777 WARNING @ Tue, 02 Aug 2022 11:59:02: Fewer paired peaks (777) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 777 pairs to build model! INFO @ Tue, 02 Aug 2022 11:59:02: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:02: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:02: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:02: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:02: #2 predicted fragment length is 12 bps INFO @ Tue, 02 Aug 2022 11:59:02: #2 alternative fragment length(s) may be 4,12,41 bps INFO @ Tue, 02 Aug 2022 11:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.20_model.r WARNING @ Tue, 02 Aug 2022 11:59:02: #2 Since the d (12) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:59:02: #2 You may need to consider one of the other alternative d(s): 4,12,41 WARNING @ Tue, 02 Aug 2022 11:59:02: #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 11:59:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.20_peaks.narrowPeak BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178856/SRX12178856.20_summits.bed INFO @ Tue, 02 Aug 2022 11:59:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling