Job ID = 16439412 SRX = SRX11245076 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:05:37 prefetch.2.10.7: 1) Downloading 'SRR14932341'... 2022-08-02T06:05:37 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:07:50 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:07:50 prefetch.2.10.7: 1) 'SRR14932341' was downloaded successfully 2022-08-02T06:07:50 prefetch.2.10.7: 'SRR14932341' has 0 unresolved dependencies Read 23622250 spots for SRR14932341/SRR14932341.sra Written 23622250 spots for SRR14932341/SRR14932341.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440224 ("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: 02:15:00 23622250 reads; of these: 23622250 (100.00%) were paired; of these: 8283815 (35.07%) aligned concordantly 0 times 10715842 (45.36%) aligned concordantly exactly 1 time 4622593 (19.57%) aligned concordantly >1 times ---- 8283815 pairs aligned concordantly 0 times; of these: 2435288 (29.40%) aligned discordantly 1 time ---- 5848527 pairs aligned 0 times concordantly or discordantly; of these: 11697054 mates make up the pairs; of these: 9155546 (78.27%) aligned 0 times 651925 (5.57%) aligned exactly 1 time 1889583 (16.15%) aligned >1 times 80.62% overall alignment rate Time searching: 02:15:00 Overall time: 02:15:00 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 28 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] 4183738 / 17635025 = 0.2372 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 17:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.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 17:43:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:43:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:44:03: 1000000 INFO @ Tue, 02 Aug 2022 17:44:13: 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 17:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.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 17:44:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:44:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:44:23: 3000000 INFO @ Tue, 02 Aug 2022 17:44:33: 1000000 INFO @ Tue, 02 Aug 2022 17:44:34: 4000000 INFO @ Tue, 02 Aug 2022 17:44:41: 2000000 INFO @ Tue, 02 Aug 2022 17:44:44: 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 17:44:50: 3000000 INFO @ Tue, 02 Aug 2022 17:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.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 17:44:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:44:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:44:55: 6000000 INFO @ Tue, 02 Aug 2022 17:45:00: 4000000 INFO @ Tue, 02 Aug 2022 17:45:04: 1000000 INFO @ Tue, 02 Aug 2022 17:45:07: 7000000 INFO @ Tue, 02 Aug 2022 17:45:10: 5000000 INFO @ Tue, 02 Aug 2022 17:45:18: 2000000 INFO @ Tue, 02 Aug 2022 17:45:18: 8000000 INFO @ Tue, 02 Aug 2022 17:45:20: 6000000 INFO @ Tue, 02 Aug 2022 17:45:30: 7000000 INFO @ Tue, 02 Aug 2022 17:45:31: 9000000 INFO @ Tue, 02 Aug 2022 17:45:31: 3000000 INFO @ Tue, 02 Aug 2022 17:45:40: 8000000 INFO @ Tue, 02 Aug 2022 17:45:43: 10000000 INFO @ Tue, 02 Aug 2022 17:45:44: 4000000 INFO @ Tue, 02 Aug 2022 17:45:49: 9000000 INFO @ Tue, 02 Aug 2022 17:45:55: 11000000 INFO @ Tue, 02 Aug 2022 17:45:57: 5000000 INFO @ Tue, 02 Aug 2022 17:45:59: 10000000 INFO @ Tue, 02 Aug 2022 17:46:07: 12000000 INFO @ Tue, 02 Aug 2022 17:46:08: 11000000 INFO @ Tue, 02 Aug 2022 17:46:10: 6000000 INFO @ Tue, 02 Aug 2022 17:46:18: 12000000 INFO @ Tue, 02 Aug 2022 17:46:18: 13000000 INFO @ Tue, 02 Aug 2022 17:46:24: 7000000 INFO @ Tue, 02 Aug 2022 17:46:27: 13000000 INFO @ Tue, 02 Aug 2022 17:46:29: 14000000 INFO @ Tue, 02 Aug 2022 17:46:36: 14000000 INFO @ Tue, 02 Aug 2022 17:46:37: 8000000 INFO @ Tue, 02 Aug 2022 17:46:41: 15000000 INFO @ Tue, 02 Aug 2022 17:46:45: 15000000 INFO @ Tue, 02 Aug 2022 17:46:50: 9000000 INFO @ Tue, 02 Aug 2022 17:46:52: 16000000 INFO @ Tue, 02 Aug 2022 17:46:54: 16000000 INFO @ Tue, 02 Aug 2022 17:47:03: 17000000 INFO @ Tue, 02 Aug 2022 17:47:04: 17000000 INFO @ Tue, 02 Aug 2022 17:47:04: 10000000 INFO @ Tue, 02 Aug 2022 17:47:12: 18000000 INFO @ Tue, 02 Aug 2022 17:47:16: 18000000 INFO @ Tue, 02 Aug 2022 17:47:18: 11000000 INFO @ Tue, 02 Aug 2022 17:47:23: 19000000 INFO @ Tue, 02 Aug 2022 17:47:27: 19000000 INFO @ Tue, 02 Aug 2022 17:47:31: 12000000 INFO @ Tue, 02 Aug 2022 17:47:33: 20000000 INFO @ Tue, 02 Aug 2022 17:47:38: 20000000 INFO @ Tue, 02 Aug 2022 17:47:43: 21000000 INFO @ Tue, 02 Aug 2022 17:47:46: 13000000 INFO @ Tue, 02 Aug 2022 17:47:49: 21000000 INFO @ Tue, 02 Aug 2022 17:47:53: 22000000 INFO @ Tue, 02 Aug 2022 17:47:59: 14000000 INFO @ Tue, 02 Aug 2022 17:48:01: 22000000 INFO @ Tue, 02 Aug 2022 17:48:03: 23000000 INFO @ Tue, 02 Aug 2022 17:48:12: 15000000 INFO @ Tue, 02 Aug 2022 17:48:12: 24000000 INFO @ Tue, 02 Aug 2022 17:48:13: 23000000 INFO @ Tue, 02 Aug 2022 17:48:21: 25000000 INFO @ Tue, 02 Aug 2022 17:48:24: 24000000 INFO @ Tue, 02 Aug 2022 17:48:24: 16000000 INFO @ Tue, 02 Aug 2022 17:48:31: 26000000 INFO @ Tue, 02 Aug 2022 17:48:36: 25000000 INFO @ Tue, 02 Aug 2022 17:48:37: 17000000 INFO @ Tue, 02 Aug 2022 17:48:41: 27000000 INFO @ Tue, 02 Aug 2022 17:48:48: 26000000 INFO @ Tue, 02 Aug 2022 17:48:50: 18000000 INFO @ Tue, 02 Aug 2022 17:48:52: 28000000 INFO @ Tue, 02 Aug 2022 17:49:00: 27000000 INFO @ Tue, 02 Aug 2022 17:49:04: 29000000 INFO @ Tue, 02 Aug 2022 17:49:04: 19000000 INFO @ Tue, 02 Aug 2022 17:49:11: 28000000 INFO @ Tue, 02 Aug 2022 17:49:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:49:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:49:14: #1 total tags in treatment: 11688177 INFO @ Tue, 02 Aug 2022 17:49:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:49:14: #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 17:49:14: #1 tags after filtering in treatment: 11032212 INFO @ Tue, 02 Aug 2022 17:49:14: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 17:49:14: #1 finished! INFO @ Tue, 02 Aug 2022 17:49:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:49:15: #2 number of paired peaks: 247 WARNING @ Tue, 02 Aug 2022 17:49:15: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 02 Aug 2022 17:49:15: start model_add_line... INFO @ Tue, 02 Aug 2022 17:49:15: start X-correlation... INFO @ Tue, 02 Aug 2022 17:49:15: end of X-cor INFO @ Tue, 02 Aug 2022 17:49:15: #2 finished! INFO @ Tue, 02 Aug 2022 17:49:15: #2 predicted fragment length is 188 bps INFO @ Tue, 02 Aug 2022 17:49:15: #2 alternative fragment length(s) may be 188 bps INFO @ Tue, 02 Aug 2022 17:49:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.10_model.r WARNING @ Tue, 02 Aug 2022 17:49:15: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:49:15: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Tue, 02 Aug 2022 17:49:15: #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 17:49:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:49:17: 20000000 INFO @ Tue, 02 Aug 2022 17:49:22: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:49:29: 21000000 INFO @ Tue, 02 Aug 2022 17:49:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:49:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:49:30: #1 total tags in treatment: 11688177 INFO @ Tue, 02 Aug 2022 17:49:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:49:30: #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 17:49:30: #1 tags after filtering in treatment: 11032212 INFO @ Tue, 02 Aug 2022 17:49:30: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 17:49:30: #1 finished! INFO @ Tue, 02 Aug 2022 17:49:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:49:31: #2 number of paired peaks: 247 WARNING @ Tue, 02 Aug 2022 17:49:31: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 02 Aug 2022 17:49:31: start model_add_line... INFO @ Tue, 02 Aug 2022 17:49:31: start X-correlation... INFO @ Tue, 02 Aug 2022 17:49:31: end of X-cor INFO @ Tue, 02 Aug 2022 17:49:31: #2 finished! INFO @ Tue, 02 Aug 2022 17:49:31: #2 predicted fragment length is 188 bps INFO @ Tue, 02 Aug 2022 17:49:31: #2 alternative fragment length(s) may be 188 bps INFO @ Tue, 02 Aug 2022 17:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.05_model.r WARNING @ Tue, 02 Aug 2022 17:49:31: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:49:31: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Tue, 02 Aug 2022 17:49:31: #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 17:49:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:49:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:49:39: 22000000 INFO @ Tue, 02 Aug 2022 17:49:47: 23000000 INFO @ Tue, 02 Aug 2022 17:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.10_summits.bed INFO @ Tue, 02 Aug 2022 17:49:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2103 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:49:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:49:55: 24000000 INFO @ Tue, 02 Aug 2022 17:50:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:50:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:50:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.05_summits.bed INFO @ Tue, 02 Aug 2022 17:50:04: Done! INFO @ Tue, 02 Aug 2022 17:50:04: 25000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4060 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:50:12: 26000000 INFO @ Tue, 02 Aug 2022 17:50:20: 27000000 INFO @ Tue, 02 Aug 2022 17:50:28: 28000000 INFO @ Tue, 02 Aug 2022 17:50:36: 29000000 INFO @ Tue, 02 Aug 2022 17:50:42: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:50:42: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:50:42: #1 total tags in treatment: 11688177 INFO @ Tue, 02 Aug 2022 17:50:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:50:42: #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 17:50:42: #1 tags after filtering in treatment: 11032212 INFO @ Tue, 02 Aug 2022 17:50:42: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 17:50:42: #1 finished! INFO @ Tue, 02 Aug 2022 17:50:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:50:43: #2 number of paired peaks: 247 WARNING @ Tue, 02 Aug 2022 17:50:43: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 02 Aug 2022 17:50:43: start model_add_line... INFO @ Tue, 02 Aug 2022 17:50:43: start X-correlation... INFO @ Tue, 02 Aug 2022 17:50:43: end of X-cor INFO @ Tue, 02 Aug 2022 17:50:43: #2 finished! INFO @ Tue, 02 Aug 2022 17:50:43: #2 predicted fragment length is 188 bps INFO @ Tue, 02 Aug 2022 17:50:43: #2 alternative fragment length(s) may be 188 bps INFO @ Tue, 02 Aug 2022 17:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.20_model.r WARNING @ Tue, 02 Aug 2022 17:50:43: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:50:43: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Tue, 02 Aug 2022 17:50:43: #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 17:50:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:50:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:51:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245076/SRX11245076.20_summits.bed INFO @ Tue, 02 Aug 2022 17:51:16: Done! pass1 - making usageList (13 chroms): 6 millis pass2 - checking and writing primary data (880 records, 4 fields): 51 millis CompletedMACS2peakCalling