Job ID = 6529707 SRX = SRX3981713 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:05 37759427 reads; of these: 37759427 (100.00%) were unpaired; of these: 1379976 (3.65%) aligned 0 times 27267385 (72.21%) aligned exactly 1 time 9112066 (24.13%) aligned >1 times 96.35% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 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] 5924470 / 36379451 = 0.1629 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 02:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.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 02:56:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:08: 1000000 INFO @ Tue, 30 Jun 2020 02:56:14: 2000000 INFO @ Tue, 30 Jun 2020 02:56:20: 3000000 INFO @ Tue, 30 Jun 2020 02:56:26: 4000000 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 02:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.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 02:56:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:33: 5000000 INFO @ Tue, 30 Jun 2020 02:56:39: 1000000 INFO @ Tue, 30 Jun 2020 02:56:40: 6000000 INFO @ Tue, 30 Jun 2020 02:56:47: 2000000 INFO @ Tue, 30 Jun 2020 02:56:48: 7000000 INFO @ Tue, 30 Jun 2020 02:56:55: 3000000 INFO @ Tue, 30 Jun 2020 02:56:55: 8000000 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 02:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.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 02:57:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:03: 4000000 INFO @ Tue, 30 Jun 2020 02:57:03: 9000000 INFO @ Tue, 30 Jun 2020 02:57:09: 1000000 INFO @ Tue, 30 Jun 2020 02:57:11: 5000000 INFO @ Tue, 30 Jun 2020 02:57:11: 10000000 INFO @ Tue, 30 Jun 2020 02:57:17: 2000000 INFO @ Tue, 30 Jun 2020 02:57:19: 11000000 INFO @ Tue, 30 Jun 2020 02:57:19: 6000000 INFO @ Tue, 30 Jun 2020 02:57:25: 3000000 INFO @ Tue, 30 Jun 2020 02:57:26: 12000000 INFO @ Tue, 30 Jun 2020 02:57:27: 7000000 INFO @ Tue, 30 Jun 2020 02:57:33: 4000000 INFO @ Tue, 30 Jun 2020 02:57:34: 13000000 INFO @ Tue, 30 Jun 2020 02:57:35: 8000000 INFO @ Tue, 30 Jun 2020 02:57:40: 5000000 INFO @ Tue, 30 Jun 2020 02:57:42: 14000000 INFO @ Tue, 30 Jun 2020 02:57:43: 9000000 INFO @ Tue, 30 Jun 2020 02:57:48: 6000000 INFO @ Tue, 30 Jun 2020 02:57:50: 15000000 INFO @ Tue, 30 Jun 2020 02:57:51: 10000000 INFO @ Tue, 30 Jun 2020 02:57:56: 7000000 INFO @ Tue, 30 Jun 2020 02:57:57: 16000000 INFO @ Tue, 30 Jun 2020 02:58:00: 11000000 INFO @ Tue, 30 Jun 2020 02:58:04: 8000000 INFO @ Tue, 30 Jun 2020 02:58:05: 17000000 INFO @ Tue, 30 Jun 2020 02:58:08: 12000000 INFO @ Tue, 30 Jun 2020 02:58:11: 9000000 INFO @ Tue, 30 Jun 2020 02:58:13: 18000000 INFO @ Tue, 30 Jun 2020 02:58:16: 13000000 INFO @ Tue, 30 Jun 2020 02:58:19: 10000000 INFO @ Tue, 30 Jun 2020 02:58:20: 19000000 INFO @ Tue, 30 Jun 2020 02:58:24: 14000000 INFO @ Tue, 30 Jun 2020 02:58:27: 11000000 INFO @ Tue, 30 Jun 2020 02:58:28: 20000000 INFO @ Tue, 30 Jun 2020 02:58:32: 15000000 INFO @ Tue, 30 Jun 2020 02:58:34: 12000000 INFO @ Tue, 30 Jun 2020 02:58:36: 21000000 INFO @ Tue, 30 Jun 2020 02:58:40: 16000000 INFO @ Tue, 30 Jun 2020 02:58:42: 13000000 INFO @ Tue, 30 Jun 2020 02:58:43: 22000000 INFO @ Tue, 30 Jun 2020 02:58:48: 17000000 INFO @ Tue, 30 Jun 2020 02:58:49: 14000000 INFO @ Tue, 30 Jun 2020 02:58:51: 23000000 INFO @ Tue, 30 Jun 2020 02:58:56: 18000000 INFO @ Tue, 30 Jun 2020 02:58:57: 15000000 INFO @ Tue, 30 Jun 2020 02:58:59: 24000000 INFO @ Tue, 30 Jun 2020 02:59:04: 19000000 INFO @ Tue, 30 Jun 2020 02:59:05: 16000000 INFO @ Tue, 30 Jun 2020 02:59:06: 25000000 INFO @ Tue, 30 Jun 2020 02:59:12: 17000000 INFO @ Tue, 30 Jun 2020 02:59:13: 20000000 INFO @ Tue, 30 Jun 2020 02:59:14: 26000000 INFO @ Tue, 30 Jun 2020 02:59:20: 18000000 INFO @ Tue, 30 Jun 2020 02:59:21: 21000000 INFO @ Tue, 30 Jun 2020 02:59:22: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:59:28: 19000000 INFO @ Tue, 30 Jun 2020 02:59:29: 22000000 INFO @ Tue, 30 Jun 2020 02:59:30: 28000000 INFO @ Tue, 30 Jun 2020 02:59:35: 20000000 INFO @ Tue, 30 Jun 2020 02:59:37: 23000000 INFO @ Tue, 30 Jun 2020 02:59:38: 29000000 INFO @ Tue, 30 Jun 2020 02:59:43: 21000000 INFO @ Tue, 30 Jun 2020 02:59:45: 24000000 INFO @ Tue, 30 Jun 2020 02:59:46: 30000000 INFO @ Tue, 30 Jun 2020 02:59:49: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:59:49: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:59:49: #1 total tags in treatment: 30454981 INFO @ Tue, 30 Jun 2020 02:59:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:49: #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 02:59:50: #1 tags after filtering in treatment: 30454935 INFO @ Tue, 30 Jun 2020 02:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:51: 22000000 INFO @ Tue, 30 Jun 2020 02:59:52: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 02:59:52: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:53: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:59:53: #2 alternative fragment length(s) may be 1,51 bps INFO @ Tue, 30 Jun 2020 02:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:53: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:53: #2 You may need to consider one of the other alternative d(s): 1,51 WARNING @ Tue, 30 Jun 2020 02:59:53: #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 02:59:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:54: 25000000 INFO @ Tue, 30 Jun 2020 02:59:58: 23000000 INFO @ Tue, 30 Jun 2020 03:00:03: 26000000 INFO @ Tue, 30 Jun 2020 03:00:06: 24000000 INFO @ Tue, 30 Jun 2020 03:00:11: 27000000 INFO @ Tue, 30 Jun 2020 03:00:14: 25000000 INFO @ Tue, 30 Jun 2020 03:00:19: 28000000 INFO @ Tue, 30 Jun 2020 03:00:22: 26000000 INFO @ Tue, 30 Jun 2020 03:00:28: 29000000 INFO @ Tue, 30 Jun 2020 03:00:29: 27000000 INFO @ Tue, 30 Jun 2020 03:00:36: 30000000 INFO @ Tue, 30 Jun 2020 03:00:37: 28000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:00:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:40: #1 total tags in treatment: 30454981 INFO @ Tue, 30 Jun 2020 03:00:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:40: #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 03:00:41: #1 tags after filtering in treatment: 30454935 INFO @ Tue, 30 Jun 2020 03:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:43: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 03:00:43: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:43: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:00:43: #2 alternative fragment length(s) may be 1,51 bps INFO @ Tue, 30 Jun 2020 03:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.10_model.r WARNING @ Tue, 30 Jun 2020 03:00:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:00:43: #2 You may need to consider one of the other alternative d(s): 1,51 WARNING @ Tue, 30 Jun 2020 03:00:43: #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 03:00:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:44: 29000000 INFO @ Tue, 30 Jun 2020 03:00:51: 30000000 INFO @ Tue, 30 Jun 2020 03:00:54: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:54: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:54: #1 total tags in treatment: 30454981 INFO @ Tue, 30 Jun 2020 03:00:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:54: #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 03:00:55: #1 tags after filtering in treatment: 30454935 INFO @ Tue, 30 Jun 2020 03:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:57: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 03:00:57: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:58: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:58: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:00:58: #2 alternative fragment length(s) may be 1,51 bps INFO @ Tue, 30 Jun 2020 03:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:00:58: #2 You may need to consider one of the other alternative d(s): 1,51 WARNING @ Tue, 30 Jun 2020 03:00:58: #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 03:00:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.05_summits.bed INFO @ Tue, 30 Jun 2020 03:01:25: Done! pass1 - making usageList (628 chroms): 2 millis pass2 - checking and writing primary data (4387 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:01:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:02:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.10_summits.bed INFO @ Tue, 30 Jun 2020 03:02:14: Done! pass1 - making usageList (468 chroms): 1 millis pass2 - checking and writing primary data (1926 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:02:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:02:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:02:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981713/SRX3981713.20_summits.bed INFO @ Tue, 30 Jun 2020 03:02:31: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (686 records, 4 fields): 9 millis CompletedMACS2peakCalling