Job ID = 6529684 SRX = SRX3981661 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: 00:14:05 45522914 reads; of these: 45522914 (100.00%) were unpaired; of these: 1942669 (4.27%) aligned 0 times 32161779 (70.65%) aligned exactly 1 time 11418466 (25.08%) aligned >1 times 95.73% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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 20 files... [bam_rmdupse_core] 6390906 / 43580245 = 0.1466 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 02:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.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 02:58:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:42: 1000000 INFO @ Tue, 30 Jun 2020 02:58:48: 2000000 INFO @ Tue, 30 Jun 2020 02:58:53: 3000000 INFO @ Tue, 30 Jun 2020 02:58:59: 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 02:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.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 02:59:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:05: 5000000 INFO @ Tue, 30 Jun 2020 02:59:12: 6000000 INFO @ Tue, 30 Jun 2020 02:59:13: 1000000 INFO @ Tue, 30 Jun 2020 02:59:19: 7000000 INFO @ Tue, 30 Jun 2020 02:59:20: 2000000 INFO @ Tue, 30 Jun 2020 02:59:26: 8000000 INFO @ Tue, 30 Jun 2020 02:59:28: 3000000 INFO @ Tue, 30 Jun 2020 02:59:33: 9000000 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 02:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.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 02:59:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:36: 4000000 INFO @ Tue, 30 Jun 2020 02:59:40: 10000000 INFO @ Tue, 30 Jun 2020 02:59:43: 1000000 INFO @ Tue, 30 Jun 2020 02:59:44: 5000000 INFO @ Tue, 30 Jun 2020 02:59:47: 11000000 INFO @ Tue, 30 Jun 2020 02:59:50: 2000000 INFO @ Tue, 30 Jun 2020 02:59:51: 6000000 INFO @ Tue, 30 Jun 2020 02:59:54: 12000000 INFO @ Tue, 30 Jun 2020 02:59:57: 3000000 INFO @ Tue, 30 Jun 2020 02:59:59: 7000000 INFO @ Tue, 30 Jun 2020 03:00:01: 13000000 INFO @ Tue, 30 Jun 2020 03:00:04: 4000000 INFO @ Tue, 30 Jun 2020 03:00:07: 8000000 INFO @ Tue, 30 Jun 2020 03:00:08: 14000000 INFO @ Tue, 30 Jun 2020 03:00:11: 5000000 INFO @ Tue, 30 Jun 2020 03:00:15: 9000000 INFO @ Tue, 30 Jun 2020 03:00:15: 15000000 INFO @ Tue, 30 Jun 2020 03:00:18: 6000000 INFO @ Tue, 30 Jun 2020 03:00:22: 16000000 INFO @ Tue, 30 Jun 2020 03:00:23: 10000000 INFO @ Tue, 30 Jun 2020 03:00:25: 7000000 INFO @ Tue, 30 Jun 2020 03:00:29: 17000000 INFO @ Tue, 30 Jun 2020 03:00:31: 11000000 INFO @ Tue, 30 Jun 2020 03:00:32: 8000000 INFO @ Tue, 30 Jun 2020 03:00:36: 18000000 INFO @ Tue, 30 Jun 2020 03:00:38: 12000000 INFO @ Tue, 30 Jun 2020 03:00:39: 9000000 INFO @ Tue, 30 Jun 2020 03:00:43: 19000000 INFO @ Tue, 30 Jun 2020 03:00:46: 10000000 INFO @ Tue, 30 Jun 2020 03:00:46: 13000000 INFO @ Tue, 30 Jun 2020 03:00:50: 20000000 INFO @ Tue, 30 Jun 2020 03:00:53: 11000000 INFO @ Tue, 30 Jun 2020 03:00:54: 14000000 INFO @ Tue, 30 Jun 2020 03:00:57: 21000000 INFO @ Tue, 30 Jun 2020 03:01:00: 12000000 INFO @ Tue, 30 Jun 2020 03:01:01: 15000000 INFO @ Tue, 30 Jun 2020 03:01:04: 22000000 INFO @ Tue, 30 Jun 2020 03:01:06: 13000000 INFO @ Tue, 30 Jun 2020 03:01:09: 16000000 INFO @ Tue, 30 Jun 2020 03:01:11: 23000000 INFO @ Tue, 30 Jun 2020 03:01:13: 14000000 INFO @ Tue, 30 Jun 2020 03:01:17: 17000000 INFO @ Tue, 30 Jun 2020 03:01:18: 24000000 INFO @ Tue, 30 Jun 2020 03:01:20: 15000000 INFO @ Tue, 30 Jun 2020 03:01:24: 18000000 INFO @ Tue, 30 Jun 2020 03:01:25: 25000000 INFO @ Tue, 30 Jun 2020 03:01:27: 16000000 INFO @ Tue, 30 Jun 2020 03:01:32: 19000000 INFO @ Tue, 30 Jun 2020 03:01:32: 26000000 INFO @ Tue, 30 Jun 2020 03:01:34: 17000000 INFO @ Tue, 30 Jun 2020 03:01:39: 27000000 INFO @ Tue, 30 Jun 2020 03:01:40: 20000000 INFO @ Tue, 30 Jun 2020 03:01:41: 18000000 INFO @ Tue, 30 Jun 2020 03:01:46: 28000000 INFO @ Tue, 30 Jun 2020 03:01:47: 21000000 INFO @ Tue, 30 Jun 2020 03:01:48: 19000000 INFO @ Tue, 30 Jun 2020 03:01:53: 29000000 INFO @ Tue, 30 Jun 2020 03:01:55: 20000000 INFO @ Tue, 30 Jun 2020 03:01:55: 22000000 INFO @ Tue, 30 Jun 2020 03:02:00: 30000000 INFO @ Tue, 30 Jun 2020 03:02:02: 21000000 INFO @ Tue, 30 Jun 2020 03:02:02: 23000000 INFO @ Tue, 30 Jun 2020 03:02:07: 31000000 INFO @ Tue, 30 Jun 2020 03:02:09: 22000000 INFO @ Tue, 30 Jun 2020 03:02:10: 24000000 INFO @ Tue, 30 Jun 2020 03:02:15: 32000000 INFO @ Tue, 30 Jun 2020 03:02:15: 23000000 INFO @ Tue, 30 Jun 2020 03:02:18: 25000000 INFO @ Tue, 30 Jun 2020 03:02:22: 33000000 INFO @ Tue, 30 Jun 2020 03:02:22: 24000000 INFO @ Tue, 30 Jun 2020 03:02:25: 26000000 INFO @ Tue, 30 Jun 2020 03:02:29: 25000000 INFO @ Tue, 30 Jun 2020 03:02:29: 34000000 INFO @ Tue, 30 Jun 2020 03:02:33: 27000000 INFO @ Tue, 30 Jun 2020 03:02:35: 26000000 INFO @ Tue, 30 Jun 2020 03:02:35: 35000000 INFO @ Tue, 30 Jun 2020 03:02:41: 28000000 INFO @ Tue, 30 Jun 2020 03:02:42: 27000000 INFO @ Tue, 30 Jun 2020 03:02:42: 36000000 INFO @ Tue, 30 Jun 2020 03:02:48: 29000000 INFO @ Tue, 30 Jun 2020 03:02:49: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:02:50: 37000000 INFO @ Tue, 30 Jun 2020 03:02:51: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:02:51: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:02:51: #1 total tags in treatment: 37189339 INFO @ Tue, 30 Jun 2020 03:02:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:51: #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 03:02:52: #1 tags after filtering in treatment: 37189288 INFO @ Tue, 30 Jun 2020 03:02:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:52: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:02:55: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 03:02:55: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:55: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:55: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:55: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:55: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:55: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:02:55: #2 alternative fragment length(s) may be 0,54,76,579 bps INFO @ Tue, 30 Jun 2020 03:02:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.05_model.r WARNING @ Tue, 30 Jun 2020 03:02:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:02:55: #2 You may need to consider one of the other alternative d(s): 0,54,76,579 WARNING @ Tue, 30 Jun 2020 03:02:55: #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 03:02:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:55: 29000000 INFO @ Tue, 30 Jun 2020 03:02:56: 30000000 INFO @ Tue, 30 Jun 2020 03:03:02: 30000000 INFO @ Tue, 30 Jun 2020 03:03:04: 31000000 INFO @ Tue, 30 Jun 2020 03:03:08: 31000000 INFO @ Tue, 30 Jun 2020 03:03:11: 32000000 INFO @ Tue, 30 Jun 2020 03:03:15: 32000000 INFO @ Tue, 30 Jun 2020 03:03:19: 33000000 INFO @ Tue, 30 Jun 2020 03:03:22: 33000000 INFO @ Tue, 30 Jun 2020 03:03:27: 34000000 INFO @ Tue, 30 Jun 2020 03:03:28: 34000000 INFO @ Tue, 30 Jun 2020 03:03:34: 35000000 INFO @ Tue, 30 Jun 2020 03:03:35: 35000000 INFO @ Tue, 30 Jun 2020 03:03:42: 36000000 INFO @ Tue, 30 Jun 2020 03:03:43: 36000000 INFO @ Tue, 30 Jun 2020 03:03:51: 37000000 INFO @ Tue, 30 Jun 2020 03:03:51: 37000000 INFO @ Tue, 30 Jun 2020 03:03:53: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:03:53: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:03:53: #1 total tags in treatment: 37189339 INFO @ Tue, 30 Jun 2020 03:03:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:03:53: #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 03:03:53: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:03:53: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:03:53: #1 total tags in treatment: 37189339 INFO @ Tue, 30 Jun 2020 03:03:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:03:53: #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 03:03:54: #1 tags after filtering in treatment: 37189288 INFO @ Tue, 30 Jun 2020 03:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:03:54: #1 finished! INFO @ Tue, 30 Jun 2020 03:03:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:54: #1 tags after filtering in treatment: 37189288 INFO @ Tue, 30 Jun 2020 03:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:03:54: #1 finished! INFO @ Tue, 30 Jun 2020 03:03:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:56: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 03:03:56: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:56: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:56: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 03:03:56: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:56: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:56: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:56: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:56: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:56: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:03:56: #2 alternative fragment length(s) may be 0,54,76,579 bps INFO @ Tue, 30 Jun 2020 03:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.20_model.r WARNING @ Tue, 30 Jun 2020 03:03:56: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:03:56: #2 You may need to consider one of the other alternative d(s): 0,54,76,579 WARNING @ Tue, 30 Jun 2020 03:03:56: #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 03:03:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:03:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:57: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:03:57: #2 alternative fragment length(s) may be 0,54,76,579 bps INFO @ Tue, 30 Jun 2020 03:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.10_model.r WARNING @ Tue, 30 Jun 2020 03:03:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:03:57: #2 You may need to consider one of the other alternative d(s): 0,54,76,579 WARNING @ Tue, 30 Jun 2020 03:03:57: #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 03:03:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:03:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.05_summits.bed INFO @ Tue, 30 Jun 2020 03:04:30: Done! pass1 - making usageList (671 chroms): 1 millis pass2 - checking and writing primary data (3392 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:05:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.20_summits.bed INFO @ Tue, 30 Jun 2020 03:05:33: Done! pass1 - making usageList (265 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981661/SRX3981661.10_summits.bed INFO @ Tue, 30 Jun 2020 03:05:35: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (1959 records, 4 fields): 18 millis CompletedMACS2peakCalling