Job ID = 6529115 SRX = ERX011406 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: 00:04:00 20779649 reads; of these: 20779649 (100.00%) were unpaired; of these: 820275 (3.95%) aligned 0 times 14766589 (71.06%) aligned exactly 1 time 5192785 (24.99%) aligned >1 times 96.05% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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 8 files... [bam_rmdupse_core] 4674165 / 19959374 = 0.2342 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 01:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.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 01:23:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:23:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:23:18: 1000000 INFO @ Tue, 30 Jun 2020 01:23:22: 2000000 INFO @ Tue, 30 Jun 2020 01:23:27: 3000000 INFO @ Tue, 30 Jun 2020 01:23:31: 4000000 INFO @ Tue, 30 Jun 2020 01:23:35: 5000000 INFO @ Tue, 30 Jun 2020 01:23:39: 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 01:23:43: 7000000 INFO @ Tue, 30 Jun 2020 01:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.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 01:23:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:23:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:23:47: 8000000 INFO @ Tue, 30 Jun 2020 01:23:49: 1000000 INFO @ Tue, 30 Jun 2020 01:23:52: 9000000 INFO @ Tue, 30 Jun 2020 01:23:54: 2000000 INFO @ Tue, 30 Jun 2020 01:23:56: 10000000 INFO @ Tue, 30 Jun 2020 01:23:59: 3000000 INFO @ Tue, 30 Jun 2020 01:24:01: 11000000 INFO @ Tue, 30 Jun 2020 01:24:04: 4000000 INFO @ Tue, 30 Jun 2020 01:24:05: 12000000 INFO @ Tue, 30 Jun 2020 01:24:09: 5000000 INFO @ Tue, 30 Jun 2020 01:24:10: 13000000 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 01:24:13: 6000000 INFO @ Tue, 30 Jun 2020 01:24:14: 14000000 INFO @ Tue, 30 Jun 2020 01:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.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 01:24:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:24:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:24:18: 7000000 INFO @ Tue, 30 Jun 2020 01:24:18: 1000000 INFO @ Tue, 30 Jun 2020 01:24:18: 15000000 INFO @ Tue, 30 Jun 2020 01:24:20: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:24:20: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:24:20: #1 total tags in treatment: 15285209 INFO @ Tue, 30 Jun 2020 01:24:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:24:20: #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 01:24:20: #1 tags after filtering in treatment: 15285208 INFO @ Tue, 30 Jun 2020 01:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:24:20: #1 finished! INFO @ Tue, 30 Jun 2020 01:24:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:24:21: #2 number of paired peaks: 576 WARNING @ Tue, 30 Jun 2020 01:24:21: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Tue, 30 Jun 2020 01:24:21: start model_add_line... INFO @ Tue, 30 Jun 2020 01:24:21: start X-correlation... INFO @ Tue, 30 Jun 2020 01:24:21: end of X-cor INFO @ Tue, 30 Jun 2020 01:24:21: #2 finished! INFO @ Tue, 30 Jun 2020 01:24:21: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:24:21: #2 alternative fragment length(s) may be 3,41,79 bps INFO @ Tue, 30 Jun 2020 01:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.05_model.r WARNING @ Tue, 30 Jun 2020 01:24:21: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:24:21: #2 You may need to consider one of the other alternative d(s): 3,41,79 WARNING @ Tue, 30 Jun 2020 01:24:21: #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 01:24:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:24:23: 2000000 INFO @ Tue, 30 Jun 2020 01:24:23: 8000000 INFO @ Tue, 30 Jun 2020 01:24:27: 3000000 INFO @ Tue, 30 Jun 2020 01:24:28: 9000000 INFO @ Tue, 30 Jun 2020 01:24:31: 4000000 INFO @ Tue, 30 Jun 2020 01:24:32: 10000000 INFO @ Tue, 30 Jun 2020 01:24:36: 5000000 INFO @ Tue, 30 Jun 2020 01:24:37: 11000000 INFO @ Tue, 30 Jun 2020 01:24:40: 6000000 INFO @ Tue, 30 Jun 2020 01:24:42: 12000000 INFO @ Tue, 30 Jun 2020 01:24:44: 7000000 INFO @ Tue, 30 Jun 2020 01:24:47: 13000000 INFO @ Tue, 30 Jun 2020 01:24:49: 8000000 INFO @ Tue, 30 Jun 2020 01:24:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:24:52: 14000000 INFO @ Tue, 30 Jun 2020 01:24:53: 9000000 INFO @ Tue, 30 Jun 2020 01:24:57: 15000000 INFO @ Tue, 30 Jun 2020 01:24:57: 10000000 INFO @ Tue, 30 Jun 2020 01:24:59: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:24:59: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:24:59: #1 total tags in treatment: 15285209 INFO @ Tue, 30 Jun 2020 01:24:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:24:59: #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 01:24:59: #1 tags after filtering in treatment: 15285208 INFO @ Tue, 30 Jun 2020 01:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:24:59: #1 finished! INFO @ Tue, 30 Jun 2020 01:24:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:25:00: #2 number of paired peaks: 576 WARNING @ Tue, 30 Jun 2020 01:25:00: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Tue, 30 Jun 2020 01:25:00: start model_add_line... INFO @ Tue, 30 Jun 2020 01:25:00: start X-correlation... INFO @ Tue, 30 Jun 2020 01:25:00: end of X-cor INFO @ Tue, 30 Jun 2020 01:25:00: #2 finished! INFO @ Tue, 30 Jun 2020 01:25:00: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:25:00: #2 alternative fragment length(s) may be 3,41,79 bps INFO @ Tue, 30 Jun 2020 01:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.10_model.r WARNING @ Tue, 30 Jun 2020 01:25:00: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:25:00: #2 You may need to consider one of the other alternative d(s): 3,41,79 WARNING @ Tue, 30 Jun 2020 01:25:00: #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 01:25:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:25:02: 11000000 INFO @ Tue, 30 Jun 2020 01:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.05_summits.bed INFO @ Tue, 30 Jun 2020 01:25:03: Done! pass1 - making usageList (640 chroms): 2 millis pass2 - checking and writing primary data (3269 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:25:06: 12000000 INFO @ Tue, 30 Jun 2020 01:25:11: 13000000 INFO @ Tue, 30 Jun 2020 01:25:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:25:19: 15000000 INFO @ Tue, 30 Jun 2020 01:25:21: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:25:21: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:25:21: #1 total tags in treatment: 15285209 INFO @ Tue, 30 Jun 2020 01:25:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:25:21: #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 01:25:21: #1 tags after filtering in treatment: 15285208 INFO @ Tue, 30 Jun 2020 01:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:25:21: #1 finished! INFO @ Tue, 30 Jun 2020 01:25:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:25:22: #2 number of paired peaks: 576 WARNING @ Tue, 30 Jun 2020 01:25:22: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Tue, 30 Jun 2020 01:25:22: start model_add_line... INFO @ Tue, 30 Jun 2020 01:25:22: start X-correlation... INFO @ Tue, 30 Jun 2020 01:25:22: end of X-cor INFO @ Tue, 30 Jun 2020 01:25:22: #2 finished! INFO @ Tue, 30 Jun 2020 01:25:22: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 01:25:22: #2 alternative fragment length(s) may be 3,41,79 bps INFO @ Tue, 30 Jun 2020 01:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.20_model.r WARNING @ Tue, 30 Jun 2020 01:25:22: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:25:22: #2 You may need to consider one of the other alternative d(s): 3,41,79 WARNING @ Tue, 30 Jun 2020 01:25:22: #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 01:25:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:25:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:25:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.10_summits.bed INFO @ Tue, 30 Jun 2020 01:25:43: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (1733 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:25:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:26:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011406/ERX011406.20_summits.bed INFO @ Tue, 30 Jun 2020 01:26:04: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 6 millis CompletedMACS2peakCalling