Job ID = 16439417 SRX = SRX11245078 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:06:20 prefetch.2.10.7: 1) Downloading 'SRR14932343'... 2022-08-02T06:06:20 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:07:12 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:07:12 prefetch.2.10.7: 1) 'SRR14932343' was downloaded successfully 2022-08-02T06:07:12 prefetch.2.10.7: 'SRR14932343' has 0 unresolved dependencies Read 26020004 spots for SRR14932343/SRR14932343.sra Written 26020004 spots for SRR14932343/SRR14932343.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440833 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:42:56 26020004 reads; of these: 26020004 (100.00%) were paired; of these: 9490786 (36.47%) aligned concordantly 0 times 11950406 (45.93%) aligned concordantly exactly 1 time 4578812 (17.60%) aligned concordantly >1 times ---- 9490786 pairs aligned concordantly 0 times; of these: 2961751 (31.21%) aligned discordantly 1 time ---- 6529035 pairs aligned 0 times concordantly or discordantly; of these: 13058070 mates make up the pairs; of these: 9902543 (75.83%) aligned 0 times 847869 (6.49%) aligned exactly 1 time 2307658 (17.67%) aligned >1 times 80.97% overall alignment rate Time searching: 02:42:57 Overall time: 02:42:57 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 32 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] 5348935 / 19420048 = 0.2754 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 18:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.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 18:18:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:18:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:18:38: 1000000 INFO @ Tue, 02 Aug 2022 18:18:49: 2000000 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 18:18:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.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 18:18:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:18:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:19:01: 3000000 INFO @ Tue, 02 Aug 2022 18:19:07: 1000000 INFO @ Tue, 02 Aug 2022 18:19:13: 4000000 INFO @ Tue, 02 Aug 2022 18:19:20: 2000000 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 18:19:25: 5000000 INFO @ Tue, 02 Aug 2022 18:19:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.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 18:19:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:19:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:19:33: 3000000 INFO @ Tue, 02 Aug 2022 18:19:38: 6000000 INFO @ Tue, 02 Aug 2022 18:19:38: 1000000 INFO @ Tue, 02 Aug 2022 18:19:46: 4000000 INFO @ Tue, 02 Aug 2022 18:19:50: 7000000 INFO @ Tue, 02 Aug 2022 18:19:50: 2000000 INFO @ Tue, 02 Aug 2022 18:19:58: 5000000 INFO @ Tue, 02 Aug 2022 18:20:03: 8000000 INFO @ Tue, 02 Aug 2022 18:20:03: 3000000 INFO @ Tue, 02 Aug 2022 18:20:11: 6000000 INFO @ Tue, 02 Aug 2022 18:20:16: 9000000 INFO @ Tue, 02 Aug 2022 18:20:16: 4000000 INFO @ Tue, 02 Aug 2022 18:20:24: 7000000 INFO @ Tue, 02 Aug 2022 18:20:29: 10000000 INFO @ Tue, 02 Aug 2022 18:20:29: 5000000 INFO @ Tue, 02 Aug 2022 18:20:36: 8000000 INFO @ Tue, 02 Aug 2022 18:20:43: 11000000 INFO @ Tue, 02 Aug 2022 18:20:42: 6000000 INFO @ Tue, 02 Aug 2022 18:20:50: 9000000 INFO @ Tue, 02 Aug 2022 18:20:55: 7000000 INFO @ Tue, 02 Aug 2022 18:20:56: 12000000 INFO @ Tue, 02 Aug 2022 18:21:03: 10000000 INFO @ Tue, 02 Aug 2022 18:21:09: 8000000 INFO @ Tue, 02 Aug 2022 18:21:09: 13000000 INFO @ Tue, 02 Aug 2022 18:21:16: 11000000 INFO @ Tue, 02 Aug 2022 18:21:21: 14000000 INFO @ Tue, 02 Aug 2022 18:21:22: 9000000 INFO @ Tue, 02 Aug 2022 18:21:29: 12000000 INFO @ Tue, 02 Aug 2022 18:21:34: 15000000 INFO @ Tue, 02 Aug 2022 18:21:35: 10000000 INFO @ Tue, 02 Aug 2022 18:21:42: 13000000 INFO @ Tue, 02 Aug 2022 18:21:47: 16000000 INFO @ Tue, 02 Aug 2022 18:21:48: 11000000 INFO @ Tue, 02 Aug 2022 18:21:55: 14000000 INFO @ Tue, 02 Aug 2022 18:21:59: 17000000 INFO @ Tue, 02 Aug 2022 18:22:01: 12000000 INFO @ Tue, 02 Aug 2022 18:22:07: 15000000 INFO @ Tue, 02 Aug 2022 18:22:12: 18000000 INFO @ Tue, 02 Aug 2022 18:22:14: 13000000 INFO @ Tue, 02 Aug 2022 18:22:20: 16000000 INFO @ Tue, 02 Aug 2022 18:22:25: 19000000 INFO @ Tue, 02 Aug 2022 18:22:26: 14000000 INFO @ Tue, 02 Aug 2022 18:22:32: 17000000 INFO @ Tue, 02 Aug 2022 18:22:38: 20000000 INFO @ Tue, 02 Aug 2022 18:22:40: 15000000 INFO @ Tue, 02 Aug 2022 18:22:45: 18000000 INFO @ Tue, 02 Aug 2022 18:22:51: 21000000 INFO @ Tue, 02 Aug 2022 18:22:52: 16000000 INFO @ Tue, 02 Aug 2022 18:22:58: 19000000 INFO @ Tue, 02 Aug 2022 18:23:04: 22000000 INFO @ Tue, 02 Aug 2022 18:23:05: 17000000 INFO @ Tue, 02 Aug 2022 18:23:10: 20000000 INFO @ Tue, 02 Aug 2022 18:23:17: 18000000 INFO @ Tue, 02 Aug 2022 18:23:17: 23000000 INFO @ Tue, 02 Aug 2022 18:23:24: 21000000 INFO @ Tue, 02 Aug 2022 18:23:30: 19000000 INFO @ Tue, 02 Aug 2022 18:23:30: 24000000 INFO @ Tue, 02 Aug 2022 18:23:37: 22000000 INFO @ Tue, 02 Aug 2022 18:23:43: 25000000 INFO @ Tue, 02 Aug 2022 18:23:43: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:23:50: 23000000 INFO @ Tue, 02 Aug 2022 18:23:56: 26000000 INFO @ Tue, 02 Aug 2022 18:23:56: 21000000 INFO @ Tue, 02 Aug 2022 18:24:03: 24000000 INFO @ Tue, 02 Aug 2022 18:24:09: 22000000 INFO @ Tue, 02 Aug 2022 18:24:14: 27000000 INFO @ Tue, 02 Aug 2022 18:24:16: 25000000 INFO @ Tue, 02 Aug 2022 18:24:22: 23000000 INFO @ Tue, 02 Aug 2022 18:24:27: 28000000 INFO @ Tue, 02 Aug 2022 18:24:28: 26000000 INFO @ Tue, 02 Aug 2022 18:24:35: 24000000 INFO @ Tue, 02 Aug 2022 18:24:41: 29000000 INFO @ Tue, 02 Aug 2022 18:24:42: 27000000 INFO @ Tue, 02 Aug 2022 18:24:48: 25000000 INFO @ Tue, 02 Aug 2022 18:24:55: 30000000 INFO @ Tue, 02 Aug 2022 18:24:56: 28000000 INFO @ Tue, 02 Aug 2022 18:25:03: 26000000 INFO @ Tue, 02 Aug 2022 18:25:08: 31000000 INFO @ Tue, 02 Aug 2022 18:25:09: 29000000 INFO @ Tue, 02 Aug 2022 18:25:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:25:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:25:14: #1 total tags in treatment: 12012394 INFO @ Tue, 02 Aug 2022 18:25:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:25:14: #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 18:25:14: #1 tags after filtering in treatment: 11252434 INFO @ Tue, 02 Aug 2022 18:25:14: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 18:25:14: #1 finished! INFO @ Tue, 02 Aug 2022 18:25:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:25:15: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 18:25:15: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 18:25:15: start model_add_line... INFO @ Tue, 02 Aug 2022 18:25:15: start X-correlation... INFO @ Tue, 02 Aug 2022 18:25:16: end of X-cor INFO @ Tue, 02 Aug 2022 18:25:16: #2 finished! INFO @ Tue, 02 Aug 2022 18:25:16: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 18:25:16: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 18:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.05_model.r WARNING @ Tue, 02 Aug 2022 18:25:16: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:25:16: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 18:25:16: #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 18:25:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:25:16: 27000000 INFO @ Tue, 02 Aug 2022 18:25:21: 30000000 INFO @ Tue, 02 Aug 2022 18:25:29: 28000000 INFO @ Tue, 02 Aug 2022 18:25:33: 31000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:25:38: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:25:39: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:25:39: #1 total tags in treatment: 12012394 INFO @ Tue, 02 Aug 2022 18:25:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:25:39: #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 18:25:39: #1 tags after filtering in treatment: 11252434 INFO @ Tue, 02 Aug 2022 18:25:39: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 18:25:39: #1 finished! INFO @ Tue, 02 Aug 2022 18:25:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:25:40: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 18:25:40: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 18:25:40: start model_add_line... INFO @ Tue, 02 Aug 2022 18:25:40: start X-correlation... INFO @ Tue, 02 Aug 2022 18:25:41: end of X-cor INFO @ Tue, 02 Aug 2022 18:25:41: #2 finished! INFO @ Tue, 02 Aug 2022 18:25:41: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 18:25:41: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 18:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.10_model.r WARNING @ Tue, 02 Aug 2022 18:25:41: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:25:41: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 18:25:41: #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 18:25:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:25:41: 29000000 INFO @ Tue, 02 Aug 2022 18:25:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:25:52: 30000000 INFO @ Tue, 02 Aug 2022 18:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.05_summits.bed INFO @ Tue, 02 Aug 2022 18:25:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4819 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:26:03: 31000000 INFO @ Tue, 02 Aug 2022 18:26:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:26:08: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:26:08: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:26:08: #1 total tags in treatment: 12012394 INFO @ Tue, 02 Aug 2022 18:26:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:26:08: #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 18:26:08: #1 tags after filtering in treatment: 11252434 INFO @ Tue, 02 Aug 2022 18:26:08: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 18:26:08: #1 finished! INFO @ Tue, 02 Aug 2022 18:26:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:26:09: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 18:26:09: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 18:26:09: start model_add_line... INFO @ Tue, 02 Aug 2022 18:26:09: start X-correlation... INFO @ Tue, 02 Aug 2022 18:26:10: end of X-cor INFO @ Tue, 02 Aug 2022 18:26:10: #2 finished! INFO @ Tue, 02 Aug 2022 18:26:10: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 18:26:10: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 18:26:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.20_model.r WARNING @ Tue, 02 Aug 2022 18:26:10: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:26:10: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 18:26:10: #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 18:26:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:26:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.10_summits.bed INFO @ Tue, 02 Aug 2022 18:26:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2328 records, 4 fields): 80 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:26:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245078/SRX11245078.20_summits.bed INFO @ Tue, 02 Aug 2022 18:26:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 17 millis CompletedMACS2peakCalling