Job ID = 16438431 SRX = SRX10031704 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:27 34370847 reads; of these: 34370847 (100.00%) were unpaired; of these: 1187579 (3.46%) aligned 0 times 27944222 (81.30%) aligned exactly 1 time 5239046 (15.24%) aligned >1 times 96.54% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 8771387 / 33183268 = 0.2643 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 14:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.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 14:10:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:42: 1000000 INFO @ Tue, 02 Aug 2022 14:10:48: 2000000 INFO @ Tue, 02 Aug 2022 14:10:54: 3000000 INFO @ Tue, 02 Aug 2022 14:11:00: 4000000 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 14:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.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 14:11:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:08: 5000000 INFO @ Tue, 02 Aug 2022 14:11:13: 1000000 INFO @ Tue, 02 Aug 2022 14:11:15: 6000000 INFO @ Tue, 02 Aug 2022 14:11:20: 2000000 INFO @ Tue, 02 Aug 2022 14:11:22: 7000000 INFO @ Tue, 02 Aug 2022 14:11:28: 3000000 INFO @ Tue, 02 Aug 2022 14:11:29: 8000000 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 14:11:35: 4000000 INFO @ Tue, 02 Aug 2022 14:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.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 14:11:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:37: 9000000 INFO @ Tue, 02 Aug 2022 14:11:43: 5000000 INFO @ Tue, 02 Aug 2022 14:11:43: 1000000 INFO @ Tue, 02 Aug 2022 14:11:44: 10000000 INFO @ Tue, 02 Aug 2022 14:11:50: 6000000 INFO @ Tue, 02 Aug 2022 14:11:50: 2000000 INFO @ Tue, 02 Aug 2022 14:11:52: 11000000 INFO @ Tue, 02 Aug 2022 14:11:57: 7000000 INFO @ Tue, 02 Aug 2022 14:11:58: 3000000 INFO @ Tue, 02 Aug 2022 14:11:59: 12000000 INFO @ Tue, 02 Aug 2022 14:12:05: 8000000 INFO @ Tue, 02 Aug 2022 14:12:05: 4000000 INFO @ Tue, 02 Aug 2022 14:12:06: 13000000 INFO @ Tue, 02 Aug 2022 14:12:12: 9000000 INFO @ Tue, 02 Aug 2022 14:12:12: 5000000 INFO @ Tue, 02 Aug 2022 14:12:14: 14000000 INFO @ Tue, 02 Aug 2022 14:12:19: 10000000 INFO @ Tue, 02 Aug 2022 14:12:19: 6000000 INFO @ Tue, 02 Aug 2022 14:12:21: 15000000 INFO @ Tue, 02 Aug 2022 14:12:27: 11000000 INFO @ Tue, 02 Aug 2022 14:12:27: 7000000 INFO @ Tue, 02 Aug 2022 14:12:28: 16000000 INFO @ Tue, 02 Aug 2022 14:12:34: 8000000 INFO @ Tue, 02 Aug 2022 14:12:34: 12000000 INFO @ Tue, 02 Aug 2022 14:12:36: 17000000 INFO @ Tue, 02 Aug 2022 14:12:41: 9000000 INFO @ Tue, 02 Aug 2022 14:12:41: 13000000 INFO @ Tue, 02 Aug 2022 14:12:43: 18000000 INFO @ Tue, 02 Aug 2022 14:12:48: 10000000 INFO @ Tue, 02 Aug 2022 14:12:49: 14000000 INFO @ Tue, 02 Aug 2022 14:12:51: 19000000 INFO @ Tue, 02 Aug 2022 14:12:56: 11000000 INFO @ Tue, 02 Aug 2022 14:12:56: 15000000 INFO @ Tue, 02 Aug 2022 14:12:58: 20000000 INFO @ Tue, 02 Aug 2022 14:13:03: 12000000 INFO @ Tue, 02 Aug 2022 14:13:03: 16000000 INFO @ Tue, 02 Aug 2022 14:13:06: 21000000 INFO @ Tue, 02 Aug 2022 14:13:10: 13000000 INFO @ Tue, 02 Aug 2022 14:13:10: 17000000 INFO @ Tue, 02 Aug 2022 14:13:13: 22000000 INFO @ Tue, 02 Aug 2022 14:13:18: 14000000 INFO @ Tue, 02 Aug 2022 14:13:18: 18000000 INFO @ Tue, 02 Aug 2022 14:13:20: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:13:25: 15000000 INFO @ Tue, 02 Aug 2022 14:13:25: 19000000 INFO @ Tue, 02 Aug 2022 14:13:28: 24000000 INFO @ Tue, 02 Aug 2022 14:13:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:13:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:13:31: #1 total tags in treatment: 24411881 INFO @ Tue, 02 Aug 2022 14:13:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:31: #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 14:13:32: #1 tags after filtering in treatment: 24411760 INFO @ Tue, 02 Aug 2022 14:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:13:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:32: 16000000 INFO @ Tue, 02 Aug 2022 14:13:33: 20000000 INFO @ Tue, 02 Aug 2022 14:13:33: #2 number of paired peaks: 350 WARNING @ Tue, 02 Aug 2022 14:13:33: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 02 Aug 2022 14:13:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:33: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:33: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:33: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:33: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 14:13:33: #2 alternative fragment length(s) may be 4,131,148 bps INFO @ Tue, 02 Aug 2022 14:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.05_model.r WARNING @ Tue, 02 Aug 2022 14:13:33: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:13:33: #2 You may need to consider one of the other alternative d(s): 4,131,148 WARNING @ Tue, 02 Aug 2022 14:13:33: #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 14:13:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:39: 17000000 INFO @ Tue, 02 Aug 2022 14:13:40: 21000000 INFO @ Tue, 02 Aug 2022 14:13:46: 18000000 INFO @ Tue, 02 Aug 2022 14:13:47: 22000000 INFO @ Tue, 02 Aug 2022 14:13:53: 19000000 INFO @ Tue, 02 Aug 2022 14:13:54: 23000000 INFO @ Tue, 02 Aug 2022 14:14:00: 20000000 INFO @ Tue, 02 Aug 2022 14:14:01: 24000000 INFO @ Tue, 02 Aug 2022 14:14:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:14:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:14:04: #1 total tags in treatment: 24411881 INFO @ Tue, 02 Aug 2022 14:14:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:04: #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 14:14:05: #1 tags after filtering in treatment: 24411760 INFO @ Tue, 02 Aug 2022 14:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:14:05: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:06: #2 number of paired peaks: 350 WARNING @ Tue, 02 Aug 2022 14:14:06: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 02 Aug 2022 14:14:06: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:06: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:06: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:06: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:06: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 14:14:06: #2 alternative fragment length(s) may be 4,131,148 bps INFO @ Tue, 02 Aug 2022 14:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.10_model.r WARNING @ Tue, 02 Aug 2022 14:14:06: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:14:06: #2 You may need to consider one of the other alternative d(s): 4,131,148 WARNING @ Tue, 02 Aug 2022 14:14:06: #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 14:14:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:14:07: 21000000 INFO @ Tue, 02 Aug 2022 14:14:13: 22000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:14:19: 23000000 INFO @ Tue, 02 Aug 2022 14:14:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:25: 24000000 INFO @ Tue, 02 Aug 2022 14:14:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:14:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:14:28: #1 total tags in treatment: 24411881 INFO @ Tue, 02 Aug 2022 14:14:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:28: #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 14:14:28: #1 tags after filtering in treatment: 24411760 INFO @ Tue, 02 Aug 2022 14:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:14:28: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:30: #2 number of paired peaks: 350 WARNING @ Tue, 02 Aug 2022 14:14:30: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 02 Aug 2022 14:14:30: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:30: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:30: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 14:14:30: #2 alternative fragment length(s) may be 4,131,148 bps INFO @ Tue, 02 Aug 2022 14:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.20_model.r WARNING @ Tue, 02 Aug 2022 14:14:30: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:14:30: #2 You may need to consider one of the other alternative d(s): 4,131,148 WARNING @ Tue, 02 Aug 2022 14:14:30: #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 14:14:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.05_summits.bed INFO @ Tue, 02 Aug 2022 14:14:42: Done! pass1 - making usageList (428 chroms): 2 millis pass2 - checking and writing primary data (5912 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:14:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.10_summits.bed INFO @ Tue, 02 Aug 2022 14:15:14: Done! pass1 - making usageList (329 chroms): 2 millis pass2 - checking and writing primary data (3694 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:15:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031704/SRX10031704.20_summits.bed INFO @ Tue, 02 Aug 2022 14:15:37: Done! pass1 - making usageList (193 chroms): 2 millis pass2 - checking and writing primary data (1634 records, 4 fields): 24 millis CompletedMACS2peakCalling