Job ID = 16438028 SRX = SRX12261341 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20233404 spots for SRR15972597/SRR15972597.sra Written 20233404 spots for SRR15972597/SRR15972597.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438112 ("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: 00:16:44 20233404 reads; of these: 20233404 (100.00%) were unpaired; of these: 701693 (3.47%) aligned 0 times 12095088 (59.78%) aligned exactly 1 time 7436623 (36.75%) aligned >1 times 96.53% overall alignment rate Time searching: 00:16:44 Overall time: 00:16:44 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 8 files... [bam_rmdupse_core] 4184330 / 19531711 = 0.2142 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 13:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.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 13:42:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:42:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:42:33: 1000000 INFO @ Tue, 02 Aug 2022 13:42:46: 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 13:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.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 13:42:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:42:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:42:57: 3000000 INFO @ Tue, 02 Aug 2022 13:43:02: 1000000 INFO @ Tue, 02 Aug 2022 13:43:11: 4000000 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 13:43:16: 2000000 INFO @ Tue, 02 Aug 2022 13:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.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 13:43:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:43:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:43:23: 5000000 INFO @ Tue, 02 Aug 2022 13:43:30: 3000000 INFO @ Tue, 02 Aug 2022 13:43:33: 1000000 INFO @ Tue, 02 Aug 2022 13:43:36: 6000000 INFO @ Tue, 02 Aug 2022 13:43:44: 4000000 INFO @ Tue, 02 Aug 2022 13:43:49: 2000000 INFO @ Tue, 02 Aug 2022 13:43:49: 7000000 INFO @ Tue, 02 Aug 2022 13:43:58: 5000000 INFO @ Tue, 02 Aug 2022 13:44:02: 8000000 INFO @ Tue, 02 Aug 2022 13:44:04: 3000000 INFO @ Tue, 02 Aug 2022 13:44:13: 6000000 INFO @ Tue, 02 Aug 2022 13:44:16: 9000000 INFO @ Tue, 02 Aug 2022 13:44:19: 4000000 INFO @ Tue, 02 Aug 2022 13:44:26: 7000000 INFO @ Tue, 02 Aug 2022 13:44:28: 10000000 INFO @ Tue, 02 Aug 2022 13:44:35: 5000000 INFO @ Tue, 02 Aug 2022 13:44:40: 8000000 INFO @ Tue, 02 Aug 2022 13:44:42: 11000000 INFO @ Tue, 02 Aug 2022 13:44:51: 6000000 INFO @ Tue, 02 Aug 2022 13:44:54: 9000000 INFO @ Tue, 02 Aug 2022 13:44:57: 12000000 INFO @ Tue, 02 Aug 2022 13:45:07: 7000000 INFO @ Tue, 02 Aug 2022 13:45:07: 13000000 INFO @ Tue, 02 Aug 2022 13:45:07: 10000000 INFO @ Tue, 02 Aug 2022 13:45:20: 14000000 INFO @ Tue, 02 Aug 2022 13:45:20: 11000000 INFO @ Tue, 02 Aug 2022 13:45:22: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:45:32: 15000000 INFO @ Tue, 02 Aug 2022 13:45:34: 12000000 INFO @ Tue, 02 Aug 2022 13:45:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:45:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:45:36: #1 total tags in treatment: 15347381 INFO @ Tue, 02 Aug 2022 13:45:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:45:36: #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 13:45:37: #1 tags after filtering in treatment: 15347381 INFO @ Tue, 02 Aug 2022 13:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:45:37: #1 finished! INFO @ Tue, 02 Aug 2022 13:45:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:45:38: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 13:45:38: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 13:45:38: start model_add_line... INFO @ Tue, 02 Aug 2022 13:45:38: start X-correlation... INFO @ Tue, 02 Aug 2022 13:45:38: end of X-cor INFO @ Tue, 02 Aug 2022 13:45:38: #2 finished! INFO @ Tue, 02 Aug 2022 13:45:38: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:45:38: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.05_model.r WARNING @ Tue, 02 Aug 2022 13:45:38: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:45:38: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:45:38: #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 13:45:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:45:39: 9000000 INFO @ Tue, 02 Aug 2022 13:45:47: 13000000 INFO @ Tue, 02 Aug 2022 13:45:53: 10000000 INFO @ Tue, 02 Aug 2022 13:45:59: 14000000 INFO @ Tue, 02 Aug 2022 13:46:09: 11000000 INFO @ Tue, 02 Aug 2022 13:46:12: 15000000 INFO @ Tue, 02 Aug 2022 13:46:17: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:46:17: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:46:17: #1 total tags in treatment: 15347381 INFO @ Tue, 02 Aug 2022 13:46:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:46:17: #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 13:46:17: #1 tags after filtering in treatment: 15347381 INFO @ Tue, 02 Aug 2022 13:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:46:17: #1 finished! INFO @ Tue, 02 Aug 2022 13:46:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:46:18: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 13:46:18: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 13:46:18: start model_add_line... INFO @ Tue, 02 Aug 2022 13:46:18: start X-correlation... INFO @ Tue, 02 Aug 2022 13:46:18: end of X-cor INFO @ Tue, 02 Aug 2022 13:46:18: #2 finished! INFO @ Tue, 02 Aug 2022 13:46:18: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:46:18: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.10_model.r WARNING @ Tue, 02 Aug 2022 13:46:19: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:46:19: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:46:19: #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 13:46:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:46:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:46:24: 12000000 INFO @ Tue, 02 Aug 2022 13:46:38: 13000000 INFO @ Tue, 02 Aug 2022 13:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.05_summits.bed INFO @ Tue, 02 Aug 2022 13:46:44: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3600 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:46:53: 14000000 INFO @ Tue, 02 Aug 2022 13:47:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:47:08: 15000000 INFO @ Tue, 02 Aug 2022 13:47:12: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:47:12: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:47:12: #1 total tags in treatment: 15347381 INFO @ Tue, 02 Aug 2022 13:47:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:47:12: #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 13:47:13: #1 tags after filtering in treatment: 15347381 INFO @ Tue, 02 Aug 2022 13:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:47:13: #1 finished! INFO @ Tue, 02 Aug 2022 13:47:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:47:14: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 13:47:14: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 13:47:14: start model_add_line... INFO @ Tue, 02 Aug 2022 13:47:14: start X-correlation... INFO @ Tue, 02 Aug 2022 13:47:14: end of X-cor INFO @ Tue, 02 Aug 2022 13:47:14: #2 finished! INFO @ Tue, 02 Aug 2022 13:47:14: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:47:14: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.20_model.r WARNING @ Tue, 02 Aug 2022 13:47:14: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:47:14: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:47:14: #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 13:47:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:47:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:47:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:47:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.10_summits.bed INFO @ Tue, 02 Aug 2022 13:47:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1375 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:47:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261341/SRX12261341.20_summits.bed INFO @ Tue, 02 Aug 2022 13:48:18: Done! pass1 - making usageList (10 chroms): 6 millis pass2 - checking and writing primary data (582 records, 4 fields): 46 millis CompletedMACS2peakCalling