Job ID = 6529739 SRX = SRX4664658 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:00 29764677 reads; of these: 29764677 (100.00%) were unpaired; of these: 780710 (2.62%) aligned 0 times 20813156 (69.93%) aligned exactly 1 time 8170811 (27.45%) aligned >1 times 97.38% overall alignment rate Time searching: 00:09:00 Overall time: 00:09:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4098819 / 28983967 = 0.1414 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.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, 30 Jun 2020 03:08:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:37: 1000000 INFO @ Tue, 30 Jun 2020 03:08:41: 2000000 INFO @ Tue, 30 Jun 2020 03:08:46: 3000000 INFO @ Tue, 30 Jun 2020 03:08:50: 4000000 INFO @ Tue, 30 Jun 2020 03:08:55: 5000000 INFO @ Tue, 30 Jun 2020 03:08:59: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.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, 30 Jun 2020 03:09:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:04: 7000000 INFO @ Tue, 30 Jun 2020 03:09:08: 1000000 INFO @ Tue, 30 Jun 2020 03:09:09: 8000000 INFO @ Tue, 30 Jun 2020 03:09:13: 2000000 INFO @ Tue, 30 Jun 2020 03:09:14: 9000000 INFO @ Tue, 30 Jun 2020 03:09:18: 10000000 INFO @ Tue, 30 Jun 2020 03:09:19: 3000000 INFO @ Tue, 30 Jun 2020 03:09:23: 11000000 INFO @ Tue, 30 Jun 2020 03:09:24: 4000000 INFO @ Tue, 30 Jun 2020 03:09:28: 12000000 INFO @ Tue, 30 Jun 2020 03:09:29: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.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, 30 Jun 2020 03:09:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:33: 13000000 INFO @ Tue, 30 Jun 2020 03:09:35: 6000000 INFO @ Tue, 30 Jun 2020 03:09:37: 1000000 INFO @ Tue, 30 Jun 2020 03:09:38: 14000000 INFO @ Tue, 30 Jun 2020 03:09:40: 7000000 INFO @ Tue, 30 Jun 2020 03:09:42: 2000000 INFO @ Tue, 30 Jun 2020 03:09:43: 15000000 INFO @ Tue, 30 Jun 2020 03:09:46: 8000000 INFO @ Tue, 30 Jun 2020 03:09:47: 3000000 INFO @ Tue, 30 Jun 2020 03:09:48: 16000000 INFO @ Tue, 30 Jun 2020 03:09:51: 9000000 INFO @ Tue, 30 Jun 2020 03:09:52: 4000000 INFO @ Tue, 30 Jun 2020 03:09:53: 17000000 INFO @ Tue, 30 Jun 2020 03:09:56: 10000000 INFO @ Tue, 30 Jun 2020 03:09:57: 5000000 INFO @ Tue, 30 Jun 2020 03:09:57: 18000000 INFO @ Tue, 30 Jun 2020 03:10:02: 6000000 INFO @ Tue, 30 Jun 2020 03:10:02: 11000000 INFO @ Tue, 30 Jun 2020 03:10:02: 19000000 INFO @ Tue, 30 Jun 2020 03:10:07: 7000000 INFO @ Tue, 30 Jun 2020 03:10:07: 12000000 INFO @ Tue, 30 Jun 2020 03:10:07: 20000000 INFO @ Tue, 30 Jun 2020 03:10:12: 8000000 INFO @ Tue, 30 Jun 2020 03:10:12: 21000000 INFO @ Tue, 30 Jun 2020 03:10:13: 13000000 INFO @ Tue, 30 Jun 2020 03:10:16: 9000000 INFO @ Tue, 30 Jun 2020 03:10:17: 22000000 INFO @ Tue, 30 Jun 2020 03:10:18: 14000000 INFO @ Tue, 30 Jun 2020 03:10:21: 10000000 INFO @ Tue, 30 Jun 2020 03:10:22: 23000000 INFO @ Tue, 30 Jun 2020 03:10:23: 15000000 INFO @ Tue, 30 Jun 2020 03:10:26: 11000000 INFO @ Tue, 30 Jun 2020 03:10:27: 24000000 INFO @ Tue, 30 Jun 2020 03:10:29: 16000000 INFO @ Tue, 30 Jun 2020 03:10:31: 12000000 INFO @ Tue, 30 Jun 2020 03:10:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:10:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:10:32: #1 total tags in treatment: 24885148 INFO @ Tue, 30 Jun 2020 03:10:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:10:33: #1 tags after filtering in treatment: 24885094 INFO @ Tue, 30 Jun 2020 03:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:10:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:10:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:10:34: 17000000 INFO @ Tue, 30 Jun 2020 03:10:34: #2 number of paired peaks: 688 WARNING @ Tue, 30 Jun 2020 03:10:34: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Tue, 30 Jun 2020 03:10:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:10:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:10:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:10:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:10:34: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 03:10:34: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 30 Jun 2020 03:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.05_model.r WARNING @ Tue, 30 Jun 2020 03:10:34: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:10:34: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 30 Jun 2020 03:10:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:10:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:10:36: 13000000 INFO @ Tue, 30 Jun 2020 03:10:39: 18000000 INFO @ Tue, 30 Jun 2020 03:10:41: 14000000 INFO @ Tue, 30 Jun 2020 03:10:45: 19000000 INFO @ Tue, 30 Jun 2020 03:10:45: 15000000 INFO @ Tue, 30 Jun 2020 03:10:50: 20000000 INFO @ Tue, 30 Jun 2020 03:10:50: 16000000 INFO @ Tue, 30 Jun 2020 03:10:55: 17000000 INFO @ Tue, 30 Jun 2020 03:10:56: 21000000 INFO @ Tue, 30 Jun 2020 03:11:00: 18000000 INFO @ Tue, 30 Jun 2020 03:11:01: 22000000 INFO @ Tue, 30 Jun 2020 03:11:05: 19000000 INFO @ Tue, 30 Jun 2020 03:11:07: 23000000 INFO @ Tue, 30 Jun 2020 03:11:09: 20000000 INFO @ Tue, 30 Jun 2020 03:11:12: 24000000 INFO @ Tue, 30 Jun 2020 03:11:14: 21000000 INFO @ Tue, 30 Jun 2020 03:11:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:17: #1 total tags in treatment: 24885148 INFO @ Tue, 30 Jun 2020 03:11:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:11:18: #1 tags after filtering in treatment: 24885094 INFO @ Tue, 30 Jun 2020 03:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:18: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:19: 22000000 INFO @ Tue, 30 Jun 2020 03:11:19: #2 number of paired peaks: 688 WARNING @ Tue, 30 Jun 2020 03:11:19: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:19: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:20: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:20: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:20: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:20: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 03:11:20: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 30 Jun 2020 03:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.10_model.r WARNING @ Tue, 30 Jun 2020 03:11:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:20: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 30 Jun 2020 03:11:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:11:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:24: 23000000 INFO @ Tue, 30 Jun 2020 03:11:28: 24000000 INFO @ Tue, 30 Jun 2020 03:11:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:33: #1 total tags in treatment: 24885148 INFO @ Tue, 30 Jun 2020 03:11:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:11:33: #1 tags after filtering in treatment: 24885094 INFO @ Tue, 30 Jun 2020 03:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:35: #2 number of paired peaks: 688 WARNING @ Tue, 30 Jun 2020 03:11:35: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:35: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 03:11:35: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 30 Jun 2020 03:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.20_model.r WARNING @ Tue, 30 Jun 2020 03:11:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:35: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 30 Jun 2020 03:11:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:11:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.05_summits.bed INFO @ Tue, 30 Jun 2020 03:11:36: Done! pass1 - making usageList (621 chroms): 2 millis pass2 - checking and writing primary data (4288 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:21: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (1650 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664658/SRX4664658.20_summits.bed INFO @ Tue, 30 Jun 2020 03:12:37: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (492 records, 4 fields): 6 millis CompletedMACS2peakCalling