Job ID = 6529703 SRX = SRX3981699 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: 00:10:05 37773505 reads; of these: 37773505 (100.00%) were unpaired; of these: 1409038 (3.73%) aligned 0 times 27358222 (72.43%) aligned exactly 1 time 9006245 (23.84%) aligned >1 times 96.27% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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] 5115206 / 36364467 = 0.1407 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 02:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.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 02:52:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:07: 1000000 INFO @ Tue, 30 Jun 2020 02:52:12: 2000000 INFO @ Tue, 30 Jun 2020 02:52:16: 3000000 INFO @ Tue, 30 Jun 2020 02:52:21: 4000000 INFO @ Tue, 30 Jun 2020 02:52:25: 5000000 INFO @ Tue, 30 Jun 2020 02:52:30: 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 02:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.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 02:52:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:34: 7000000 INFO @ Tue, 30 Jun 2020 02:52:37: 1000000 INFO @ Tue, 30 Jun 2020 02:52:39: 8000000 INFO @ Tue, 30 Jun 2020 02:52:41: 2000000 INFO @ Tue, 30 Jun 2020 02:52:43: 9000000 INFO @ Tue, 30 Jun 2020 02:52:46: 3000000 INFO @ Tue, 30 Jun 2020 02:52:48: 10000000 INFO @ Tue, 30 Jun 2020 02:52:50: 4000000 INFO @ Tue, 30 Jun 2020 02:52:52: 11000000 INFO @ Tue, 30 Jun 2020 02:52:55: 5000000 INFO @ Tue, 30 Jun 2020 02:52:57: 12000000 INFO @ Tue, 30 Jun 2020 02:52:59: 6000000 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 02:53:01: 13000000 INFO @ Tue, 30 Jun 2020 02:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.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 02:53:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:04: 7000000 INFO @ Tue, 30 Jun 2020 02:53:06: 14000000 INFO @ Tue, 30 Jun 2020 02:53:07: 1000000 INFO @ Tue, 30 Jun 2020 02:53:08: 8000000 INFO @ Tue, 30 Jun 2020 02:53:10: 15000000 INFO @ Tue, 30 Jun 2020 02:53:11: 2000000 INFO @ Tue, 30 Jun 2020 02:53:13: 9000000 INFO @ Tue, 30 Jun 2020 02:53:15: 16000000 INFO @ Tue, 30 Jun 2020 02:53:16: 3000000 INFO @ Tue, 30 Jun 2020 02:53:17: 10000000 INFO @ Tue, 30 Jun 2020 02:53:19: 17000000 INFO @ Tue, 30 Jun 2020 02:53:21: 4000000 INFO @ Tue, 30 Jun 2020 02:53:22: 11000000 INFO @ Tue, 30 Jun 2020 02:53:24: 18000000 INFO @ Tue, 30 Jun 2020 02:53:25: 5000000 INFO @ Tue, 30 Jun 2020 02:53:26: 12000000 INFO @ Tue, 30 Jun 2020 02:53:28: 19000000 INFO @ Tue, 30 Jun 2020 02:53:30: 6000000 INFO @ Tue, 30 Jun 2020 02:53:31: 13000000 INFO @ Tue, 30 Jun 2020 02:53:33: 20000000 INFO @ Tue, 30 Jun 2020 02:53:34: 7000000 INFO @ Tue, 30 Jun 2020 02:53:35: 14000000 INFO @ Tue, 30 Jun 2020 02:53:37: 21000000 INFO @ Tue, 30 Jun 2020 02:53:39: 8000000 INFO @ Tue, 30 Jun 2020 02:53:40: 15000000 INFO @ Tue, 30 Jun 2020 02:53:42: 22000000 INFO @ Tue, 30 Jun 2020 02:53:43: 9000000 INFO @ Tue, 30 Jun 2020 02:53:44: 16000000 INFO @ Tue, 30 Jun 2020 02:53:46: 23000000 INFO @ Tue, 30 Jun 2020 02:53:48: 10000000 INFO @ Tue, 30 Jun 2020 02:53:49: 17000000 INFO @ Tue, 30 Jun 2020 02:53:51: 24000000 INFO @ Tue, 30 Jun 2020 02:53:52: 11000000 INFO @ Tue, 30 Jun 2020 02:53:53: 18000000 INFO @ Tue, 30 Jun 2020 02:53:55: 25000000 INFO @ Tue, 30 Jun 2020 02:53:56: 12000000 INFO @ Tue, 30 Jun 2020 02:53:57: 19000000 INFO @ Tue, 30 Jun 2020 02:54:00: 26000000 INFO @ Tue, 30 Jun 2020 02:54:01: 13000000 INFO @ Tue, 30 Jun 2020 02:54:02: 20000000 INFO @ Tue, 30 Jun 2020 02:54:05: 27000000 INFO @ Tue, 30 Jun 2020 02:54:05: 14000000 INFO @ Tue, 30 Jun 2020 02:54:06: 21000000 INFO @ Tue, 30 Jun 2020 02:54:09: 28000000 INFO @ Tue, 30 Jun 2020 02:54:10: 15000000 INFO @ Tue, 30 Jun 2020 02:54:11: 22000000 INFO @ Tue, 30 Jun 2020 02:54:14: 29000000 INFO @ Tue, 30 Jun 2020 02:54:14: 16000000 INFO @ Tue, 30 Jun 2020 02:54:15: 23000000 INFO @ Tue, 30 Jun 2020 02:54:18: 30000000 INFO @ Tue, 30 Jun 2020 02:54:19: 17000000 INFO @ Tue, 30 Jun 2020 02:54:20: 24000000 INFO @ Tue, 30 Jun 2020 02:54:23: 31000000 INFO @ Tue, 30 Jun 2020 02:54:23: 18000000 INFO @ Tue, 30 Jun 2020 02:54:24: 25000000 INFO @ Tue, 30 Jun 2020 02:54:24: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:54:24: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:54:24: #1 total tags in treatment: 31249261 INFO @ Tue, 30 Jun 2020 02:54:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:24: #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 02:54:25: #1 tags after filtering in treatment: 31249210 INFO @ Tue, 30 Jun 2020 02:54:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:27: #2 number of paired peaks: 184 WARNING @ Tue, 30 Jun 2020 02:54:27: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:27: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:54:27: #2 alternative fragment length(s) may be 1,45 bps INFO @ Tue, 30 Jun 2020 02:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.05_model.r WARNING @ Tue, 30 Jun 2020 02:54:27: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:27: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Tue, 30 Jun 2020 02:54:27: #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 02:54:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:28: 19000000 INFO @ Tue, 30 Jun 2020 02:54:29: 26000000 INFO @ Tue, 30 Jun 2020 02:54:32: 20000000 INFO @ Tue, 30 Jun 2020 02:54:33: 27000000 INFO @ Tue, 30 Jun 2020 02:54:37: 21000000 INFO @ Tue, 30 Jun 2020 02:54:38: 28000000 INFO @ Tue, 30 Jun 2020 02:54:41: 22000000 INFO @ Tue, 30 Jun 2020 02:54:42: 29000000 INFO @ Tue, 30 Jun 2020 02:54:46: 23000000 INFO @ Tue, 30 Jun 2020 02:54:47: 30000000 INFO @ Tue, 30 Jun 2020 02:54:50: 24000000 INFO @ Tue, 30 Jun 2020 02:54:51: 31000000 INFO @ Tue, 30 Jun 2020 02:54:53: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:54:53: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:54:53: #1 total tags in treatment: 31249261 INFO @ Tue, 30 Jun 2020 02:54:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:53: #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 02:54:54: #1 tags after filtering in treatment: 31249210 INFO @ Tue, 30 Jun 2020 02:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:55: 25000000 INFO @ Tue, 30 Jun 2020 02:54:56: #2 number of paired peaks: 184 WARNING @ Tue, 30 Jun 2020 02:54:56: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:56: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:56: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:56: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:56: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:54:56: #2 alternative fragment length(s) may be 1,45 bps INFO @ Tue, 30 Jun 2020 02:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.10_model.r WARNING @ Tue, 30 Jun 2020 02:54:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:56: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Tue, 30 Jun 2020 02:54:56: #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 02:54:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:59: 26000000 INFO @ Tue, 30 Jun 2020 02:55:04: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:55:08: 28000000 INFO @ Tue, 30 Jun 2020 02:55:13: 29000000 INFO @ Tue, 30 Jun 2020 02:55:17: 30000000 INFO @ Tue, 30 Jun 2020 02:55:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:22: 31000000 INFO @ Tue, 30 Jun 2020 02:55:23: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:55:23: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:55:23: #1 total tags in treatment: 31249261 INFO @ Tue, 30 Jun 2020 02:55:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:23: #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 02:55:24: #1 tags after filtering in treatment: 31249210 INFO @ Tue, 30 Jun 2020 02:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:26: #2 number of paired peaks: 184 WARNING @ Tue, 30 Jun 2020 02:55:26: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:26: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:55:26: #2 alternative fragment length(s) may be 1,45 bps INFO @ Tue, 30 Jun 2020 02:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.20_model.r WARNING @ Tue, 30 Jun 2020 02:55:26: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:26: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Tue, 30 Jun 2020 02:55:26: #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 02:55:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.05_summits.bed INFO @ Tue, 30 Jun 2020 02:55:42: Done! pass1 - making usageList (658 chroms): 1 millis pass2 - checking and writing primary data (3412 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.10_summits.bed INFO @ Tue, 30 Jun 2020 02:56:11: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1691 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:56:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981699/SRX3981699.20_summits.bed INFO @ Tue, 30 Jun 2020 02:56:41: Done! pass1 - making usageList (209 chroms): 1 millis pass2 - checking and writing primary data (509 records, 4 fields): 7 millis CompletedMACS2peakCalling