Job ID = 14168996 SRX = SRX9910786 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 40097488 spots for SRR13498857/SRR13498857.sra Written 40097488 spots for SRR13498857/SRR13498857.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170405 ("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: 02:04:35 40097488 reads; of these: 40097488 (100.00%) were paired; of these: 17404690 (43.41%) aligned concordantly 0 times 16155959 (40.29%) aligned concordantly exactly 1 time 6536839 (16.30%) aligned concordantly >1 times ---- 17404690 pairs aligned concordantly 0 times; of these: 2658167 (15.27%) aligned discordantly 1 time ---- 14746523 pairs aligned 0 times concordantly or discordantly; of these: 29493046 mates make up the pairs; of these: 24679707 (83.68%) aligned 0 times 618981 (2.10%) aligned exactly 1 time 4194358 (14.22%) aligned >1 times 69.23% overall alignment rate Time searching: 02:04:36 Overall time: 02:04:36 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 44 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] 9052439 / 25203022 = 0.3592 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 01:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.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 @ Sat, 11 Dec 2021 01:15:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 01:15:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 01:15:49: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 01:16:01: 2000000 INFO @ Sat, 11 Dec 2021 01:16:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.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 @ Sat, 11 Dec 2021 01:16:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 01:16:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 01:16:13: 3000000 INFO @ Sat, 11 Dec 2021 01:16:18: 1000000 INFO @ Sat, 11 Dec 2021 01:16:25: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 01:16:32: 2000000 INFO @ Sat, 11 Dec 2021 01:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.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 @ Sat, 11 Dec 2021 01:16:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 01:16:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 01:16:37: 5000000 INFO @ Sat, 11 Dec 2021 01:16:44: 3000000 INFO @ Sat, 11 Dec 2021 01:16:49: 6000000 INFO @ Sat, 11 Dec 2021 01:16:49: 1000000 INFO @ Sat, 11 Dec 2021 01:16:57: 4000000 INFO @ Sat, 11 Dec 2021 01:17:01: 7000000 INFO @ Sat, 11 Dec 2021 01:17:04: 2000000 INFO @ Sat, 11 Dec 2021 01:17:10: 5000000 INFO @ Sat, 11 Dec 2021 01:17:14: 8000000 INFO @ Sat, 11 Dec 2021 01:17:18: 3000000 INFO @ Sat, 11 Dec 2021 01:17:23: 6000000 INFO @ Sat, 11 Dec 2021 01:17:26: 9000000 INFO @ Sat, 11 Dec 2021 01:17:31: 4000000 INFO @ Sat, 11 Dec 2021 01:17:37: 7000000 INFO @ Sat, 11 Dec 2021 01:17:39: 10000000 INFO @ Sat, 11 Dec 2021 01:17:44: 5000000 INFO @ Sat, 11 Dec 2021 01:17:50: 8000000 INFO @ Sat, 11 Dec 2021 01:17:52: 11000000 INFO @ Sat, 11 Dec 2021 01:17:58: 6000000 INFO @ Sat, 11 Dec 2021 01:18:04: 9000000 INFO @ Sat, 11 Dec 2021 01:18:04: 12000000 INFO @ Sat, 11 Dec 2021 01:18:11: 7000000 INFO @ Sat, 11 Dec 2021 01:18:16: 10000000 INFO @ Sat, 11 Dec 2021 01:18:17: 13000000 INFO @ Sat, 11 Dec 2021 01:18:24: 8000000 INFO @ Sat, 11 Dec 2021 01:18:29: 11000000 INFO @ Sat, 11 Dec 2021 01:18:29: 14000000 INFO @ Sat, 11 Dec 2021 01:18:36: 9000000 INFO @ Sat, 11 Dec 2021 01:18:41: 12000000 INFO @ Sat, 11 Dec 2021 01:18:42: 15000000 INFO @ Sat, 11 Dec 2021 01:18:48: 10000000 INFO @ Sat, 11 Dec 2021 01:18:53: 13000000 INFO @ Sat, 11 Dec 2021 01:18:54: 16000000 INFO @ Sat, 11 Dec 2021 01:18:59: 11000000 INFO @ Sat, 11 Dec 2021 01:19:06: 14000000 INFO @ Sat, 11 Dec 2021 01:19:07: 17000000 INFO @ Sat, 11 Dec 2021 01:19:12: 12000000 INFO @ Sat, 11 Dec 2021 01:19:19: 15000000 INFO @ Sat, 11 Dec 2021 01:19:19: 18000000 INFO @ Sat, 11 Dec 2021 01:19:25: 13000000 INFO @ Sat, 11 Dec 2021 01:19:31: 16000000 INFO @ Sat, 11 Dec 2021 01:19:32: 19000000 INFO @ Sat, 11 Dec 2021 01:19:37: 14000000 INFO @ Sat, 11 Dec 2021 01:19:43: 17000000 INFO @ Sat, 11 Dec 2021 01:19:44: 20000000 INFO @ Sat, 11 Dec 2021 01:19:49: 15000000 INFO @ Sat, 11 Dec 2021 01:19:55: 18000000 INFO @ Sat, 11 Dec 2021 01:19:56: 21000000 INFO @ Sat, 11 Dec 2021 01:20:01: 16000000 INFO @ Sat, 11 Dec 2021 01:20:08: 19000000 INFO @ Sat, 11 Dec 2021 01:20:08: 22000000 INFO @ Sat, 11 Dec 2021 01:20:14: 17000000 INFO @ Sat, 11 Dec 2021 01:20:20: 20000000 INFO @ Sat, 11 Dec 2021 01:20:20: 23000000 INFO @ Sat, 11 Dec 2021 01:20:26: 18000000 INFO @ Sat, 11 Dec 2021 01:20:32: 21000000 INFO @ Sat, 11 Dec 2021 01:20:33: 24000000 INFO @ Sat, 11 Dec 2021 01:20:38: 19000000 INFO @ Sat, 11 Dec 2021 01:20:44: 25000000 INFO @ Sat, 11 Dec 2021 01:20:44: 22000000 INFO @ Sat, 11 Dec 2021 01:20:50: 20000000 INFO @ Sat, 11 Dec 2021 01:20:56: 26000000 INFO @ Sat, 11 Dec 2021 01:20:56: 23000000 INFO @ Sat, 11 Dec 2021 01:21:02: 21000000 INFO @ Sat, 11 Dec 2021 01:21:07: 27000000 INFO @ Sat, 11 Dec 2021 01:21:08: 24000000 INFO @ Sat, 11 Dec 2021 01:21:13: 22000000 INFO @ Sat, 11 Dec 2021 01:21:19: 28000000 INFO @ Sat, 11 Dec 2021 01:21:20: 25000000 INFO @ Sat, 11 Dec 2021 01:21:26: 23000000 INFO @ Sat, 11 Dec 2021 01:21:30: 29000000 INFO @ Sat, 11 Dec 2021 01:21:31: 26000000 INFO @ Sat, 11 Dec 2021 01:21:38: 24000000 INFO @ Sat, 11 Dec 2021 01:21:42: 30000000 INFO @ Sat, 11 Dec 2021 01:21:43: 27000000 INFO @ Sat, 11 Dec 2021 01:21:50: 25000000 INFO @ Sat, 11 Dec 2021 01:21:54: 28000000 INFO @ Sat, 11 Dec 2021 01:21:54: 31000000 INFO @ Sat, 11 Dec 2021 01:22:01: 26000000 INFO @ Sat, 11 Dec 2021 01:22:05: 29000000 INFO @ Sat, 11 Dec 2021 01:22:06: 32000000 INFO @ Sat, 11 Dec 2021 01:22:13: 27000000 INFO @ Sat, 11 Dec 2021 01:22:16: 30000000 INFO @ Sat, 11 Dec 2021 01:22:18: 33000000 INFO @ Sat, 11 Dec 2021 01:22:24: 28000000 INFO @ Sat, 11 Dec 2021 01:22:28: 31000000 INFO @ Sat, 11 Dec 2021 01:22:30: 34000000 INFO @ Sat, 11 Dec 2021 01:22:35: 29000000 INFO @ Sat, 11 Dec 2021 01:22:39: 32000000 INFO @ Sat, 11 Dec 2021 01:22:42: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 01:22:47: 30000000 INFO @ Sat, 11 Dec 2021 01:22:51: 33000000 INFO @ Sat, 11 Dec 2021 01:22:53: 36000000 INFO @ Sat, 11 Dec 2021 01:22:59: 31000000 INFO @ Sat, 11 Dec 2021 01:23:03: 34000000 INFO @ Sat, 11 Dec 2021 01:23:05: 37000000 INFO @ Sat, 11 Dec 2021 01:23:10: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 01:23:10: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 01:23:10: #1 total tags in treatment: 14358689 INFO @ Sat, 11 Dec 2021 01:23:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 01:23:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 01:23:10: #1 tags after filtering in treatment: 11498208 INFO @ Sat, 11 Dec 2021 01:23:10: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 01:23:10: #1 finished! INFO @ Sat, 11 Dec 2021 01:23:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 01:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 01:23:11: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 01:23:11: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 01:23:11: start model_add_line... INFO @ Sat, 11 Dec 2021 01:23:11: start X-correlation... INFO @ Sat, 11 Dec 2021 01:23:11: end of X-cor INFO @ Sat, 11 Dec 2021 01:23:11: #2 finished! INFO @ Sat, 11 Dec 2021 01:23:11: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 01:23:11: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 01:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.05_model.r WARNING @ Sat, 11 Dec 2021 01:23:11: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 01:23:11: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 01:23:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 01:23:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 01:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 01:23:12: 32000000 INFO @ Sat, 11 Dec 2021 01:23:15: 35000000 INFO @ Sat, 11 Dec 2021 01:23:24: 33000000 INFO @ Sat, 11 Dec 2021 01:23:30: 36000000 INFO @ Sat, 11 Dec 2021 01:23:36: 34000000 INFO @ Sat, 11 Dec 2021 01:23:43: 37000000 INFO @ Sat, 11 Dec 2021 01:23:47: 35000000 INFO @ Sat, 11 Dec 2021 01:23:47: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 01:23:47: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 01:23:47: #1 total tags in treatment: 14358689 INFO @ Sat, 11 Dec 2021 01:23:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 01:23:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 01:23:48: #1 tags after filtering in treatment: 11498208 INFO @ Sat, 11 Dec 2021 01:23:48: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 01:23:48: #1 finished! INFO @ Sat, 11 Dec 2021 01:23:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 01:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 01:23:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 01:23:49: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 01:23:49: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 01:23:49: start model_add_line... INFO @ Sat, 11 Dec 2021 01:23:49: start X-correlation... INFO @ Sat, 11 Dec 2021 01:23:49: end of X-cor INFO @ Sat, 11 Dec 2021 01:23:49: #2 finished! INFO @ Sat, 11 Dec 2021 01:23:49: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 01:23:49: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 01:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.10_model.r WARNING @ Sat, 11 Dec 2021 01:23:49: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 01:23:49: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 01:23:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 01:23:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 01:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 01:23:57: 36000000 INFO @ Sat, 11 Dec 2021 01:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.05_peaks.xls INFO @ Sat, 11 Dec 2021 01:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 01:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.05_summits.bed INFO @ Sat, 11 Dec 2021 01:24:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4441 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 01:24:08: 37000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 01:24:12: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 01:24:12: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 01:24:12: #1 total tags in treatment: 14358689 INFO @ Sat, 11 Dec 2021 01:24:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 01:24:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 01:24:13: #1 tags after filtering in treatment: 11498208 INFO @ Sat, 11 Dec 2021 01:24:13: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 01:24:13: #1 finished! INFO @ Sat, 11 Dec 2021 01:24:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 01:24:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 01:24:14: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 01:24:14: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 01:24:14: start model_add_line... INFO @ Sat, 11 Dec 2021 01:24:14: start X-correlation... INFO @ Sat, 11 Dec 2021 01:24:14: end of X-cor INFO @ Sat, 11 Dec 2021 01:24:14: #2 finished! INFO @ Sat, 11 Dec 2021 01:24:14: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 01:24:14: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 01:24:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.20_model.r WARNING @ Sat, 11 Dec 2021 01:24:14: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 01:24:14: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 01:24:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 01:24:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 01:24:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 01:24:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 01:24:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 01:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.10_peaks.xls INFO @ Sat, 11 Dec 2021 01:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 01:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.10_summits.bed INFO @ Sat, 11 Dec 2021 01:24:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 01:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.20_peaks.xls INFO @ Sat, 11 Dec 2021 01:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 01:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910786/SRX9910786.20_summits.bed INFO @ Sat, 11 Dec 2021 01:25:12: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 4 millis CompletedMACS2peakCalling