Job ID = 14167479 SRX = SRX8574277 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: 00:20:15 54185096 reads; of these: 54185096 (100.00%) were unpaired; of these: 8289788 (15.30%) aligned 0 times 34167860 (63.06%) aligned exactly 1 time 11727448 (21.64%) aligned >1 times 84.70% overall alignment rate Time searching: 00:20:15 Overall time: 00:20:15 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] 13206276 / 45895308 = 0.2877 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.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 @ Fri, 10 Dec 2021 12:57:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:57:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:57:15: 1000000 INFO @ Fri, 10 Dec 2021 12:57:20: 2000000 INFO @ Fri, 10 Dec 2021 12:57:26: 3000000 INFO @ Fri, 10 Dec 2021 12:57:31: 4000000 INFO @ Fri, 10 Dec 2021 12:57:36: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.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 @ Fri, 10 Dec 2021 12:57:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:57:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:57:42: 6000000 INFO @ Fri, 10 Dec 2021 12:57:45: 1000000 INFO @ Fri, 10 Dec 2021 12:57:47: 7000000 INFO @ Fri, 10 Dec 2021 12:57:51: 2000000 INFO @ Fri, 10 Dec 2021 12:57:53: 8000000 INFO @ Fri, 10 Dec 2021 12:57:56: 3000000 INFO @ Fri, 10 Dec 2021 12:57:58: 9000000 INFO @ Fri, 10 Dec 2021 12:58:02: 4000000 INFO @ Fri, 10 Dec 2021 12:58:04: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:58:08: 5000000 INFO @ Fri, 10 Dec 2021 12:58:09: 11000000 INFO @ Fri, 10 Dec 2021 12:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.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 @ Fri, 10 Dec 2021 12:58:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:58:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:58:13: 6000000 INFO @ Fri, 10 Dec 2021 12:58:15: 12000000 INFO @ Fri, 10 Dec 2021 12:58:19: 1000000 INFO @ Fri, 10 Dec 2021 12:58:19: 7000000 INFO @ Fri, 10 Dec 2021 12:58:21: 13000000 INFO @ Fri, 10 Dec 2021 12:58:25: 8000000 INFO @ Fri, 10 Dec 2021 12:58:26: 14000000 INFO @ Fri, 10 Dec 2021 12:58:28: 2000000 INFO @ Fri, 10 Dec 2021 12:58:31: 9000000 INFO @ Fri, 10 Dec 2021 12:58:32: 15000000 INFO @ Fri, 10 Dec 2021 12:58:36: 10000000 INFO @ Fri, 10 Dec 2021 12:58:37: 3000000 INFO @ Fri, 10 Dec 2021 12:58:38: 16000000 INFO @ Fri, 10 Dec 2021 12:58:42: 11000000 INFO @ Fri, 10 Dec 2021 12:58:43: 17000000 INFO @ Fri, 10 Dec 2021 12:58:46: 4000000 INFO @ Fri, 10 Dec 2021 12:58:48: 12000000 INFO @ Fri, 10 Dec 2021 12:58:49: 18000000 INFO @ Fri, 10 Dec 2021 12:58:54: 13000000 INFO @ Fri, 10 Dec 2021 12:58:55: 19000000 INFO @ Fri, 10 Dec 2021 12:58:55: 5000000 INFO @ Fri, 10 Dec 2021 12:58:59: 14000000 INFO @ Fri, 10 Dec 2021 12:59:00: 20000000 INFO @ Fri, 10 Dec 2021 12:59:04: 6000000 INFO @ Fri, 10 Dec 2021 12:59:05: 15000000 INFO @ Fri, 10 Dec 2021 12:59:06: 21000000 INFO @ Fri, 10 Dec 2021 12:59:11: 16000000 INFO @ Fri, 10 Dec 2021 12:59:12: 22000000 INFO @ Fri, 10 Dec 2021 12:59:13: 7000000 INFO @ Fri, 10 Dec 2021 12:59:17: 17000000 INFO @ Fri, 10 Dec 2021 12:59:18: 23000000 INFO @ Fri, 10 Dec 2021 12:59:21: 8000000 INFO @ Fri, 10 Dec 2021 12:59:23: 18000000 INFO @ Fri, 10 Dec 2021 12:59:23: 24000000 INFO @ Fri, 10 Dec 2021 12:59:28: 9000000 INFO @ Fri, 10 Dec 2021 12:59:29: 19000000 INFO @ Fri, 10 Dec 2021 12:59:29: 25000000 INFO @ Fri, 10 Dec 2021 12:59:34: 20000000 INFO @ Fri, 10 Dec 2021 12:59:35: 26000000 INFO @ Fri, 10 Dec 2021 12:59:36: 10000000 INFO @ Fri, 10 Dec 2021 12:59:40: 21000000 INFO @ Fri, 10 Dec 2021 12:59:41: 27000000 INFO @ Fri, 10 Dec 2021 12:59:43: 11000000 INFO @ Fri, 10 Dec 2021 12:59:46: 22000000 INFO @ Fri, 10 Dec 2021 12:59:47: 28000000 INFO @ Fri, 10 Dec 2021 12:59:51: 12000000 INFO @ Fri, 10 Dec 2021 12:59:52: 23000000 INFO @ Fri, 10 Dec 2021 12:59:53: 29000000 INFO @ Fri, 10 Dec 2021 12:59:57: 24000000 INFO @ Fri, 10 Dec 2021 12:59:58: 13000000 INFO @ Fri, 10 Dec 2021 12:59:59: 30000000 INFO @ Fri, 10 Dec 2021 13:00:03: 25000000 INFO @ Fri, 10 Dec 2021 13:00:04: 31000000 INFO @ Fri, 10 Dec 2021 13:00:06: 14000000 INFO @ Fri, 10 Dec 2021 13:00:09: 26000000 INFO @ Fri, 10 Dec 2021 13:00:10: 32000000 INFO @ Fri, 10 Dec 2021 13:00:14: 15000000 INFO @ Fri, 10 Dec 2021 13:00:15: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 13:00:15: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 13:00:15: #1 total tags in treatment: 32689032 INFO @ Fri, 10 Dec 2021 13:00:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:00:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:00:15: 27000000 INFO @ Fri, 10 Dec 2021 13:00:16: #1 tags after filtering in treatment: 32689032 INFO @ Fri, 10 Dec 2021 13:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:00:16: #1 finished! INFO @ Fri, 10 Dec 2021 13:00:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:00:18: #2 number of paired peaks: 380 WARNING @ Fri, 10 Dec 2021 13:00:18: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 10 Dec 2021 13:00:18: start model_add_line... INFO @ Fri, 10 Dec 2021 13:00:18: start X-correlation... INFO @ Fri, 10 Dec 2021 13:00:18: end of X-cor INFO @ Fri, 10 Dec 2021 13:00:18: #2 finished! INFO @ Fri, 10 Dec 2021 13:00:18: #2 predicted fragment length is 133 bps INFO @ Fri, 10 Dec 2021 13:00:18: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 10 Dec 2021 13:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.05_model.r WARNING @ Fri, 10 Dec 2021 13:00:18: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:00:18: #2 You may need to consider one of the other alternative d(s): 4,133 WARNING @ Fri, 10 Dec 2021 13:00:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:00:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:00:21: 28000000 INFO @ Fri, 10 Dec 2021 13:00:21: 16000000 INFO @ Fri, 10 Dec 2021 13:00:27: 29000000 INFO @ Fri, 10 Dec 2021 13:00:29: 17000000 INFO @ Fri, 10 Dec 2021 13:00:32: 30000000 INFO @ Fri, 10 Dec 2021 13:00:37: 18000000 INFO @ Fri, 10 Dec 2021 13:00:38: 31000000 INFO @ Fri, 10 Dec 2021 13:00:44: 32000000 INFO @ Fri, 10 Dec 2021 13:00:45: 19000000 INFO @ Fri, 10 Dec 2021 13:00:48: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 13:00:48: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 13:00:48: #1 total tags in treatment: 32689032 INFO @ Fri, 10 Dec 2021 13:00:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:00:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:00:49: #1 tags after filtering in treatment: 32689032 INFO @ Fri, 10 Dec 2021 13:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:00:49: #1 finished! INFO @ Fri, 10 Dec 2021 13:00:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:00:51: #2 number of paired peaks: 380 WARNING @ Fri, 10 Dec 2021 13:00:51: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 10 Dec 2021 13:00:51: start model_add_line... INFO @ Fri, 10 Dec 2021 13:00:52: start X-correlation... INFO @ Fri, 10 Dec 2021 13:00:52: end of X-cor INFO @ Fri, 10 Dec 2021 13:00:52: #2 finished! INFO @ Fri, 10 Dec 2021 13:00:52: #2 predicted fragment length is 133 bps INFO @ Fri, 10 Dec 2021 13:00:52: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 10 Dec 2021 13:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.10_model.r WARNING @ Fri, 10 Dec 2021 13:00:52: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:00:52: #2 You may need to consider one of the other alternative d(s): 4,133 WARNING @ Fri, 10 Dec 2021 13:00:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:00:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:00:52: 20000000 INFO @ Fri, 10 Dec 2021 13:01:00: 21000000 INFO @ Fri, 10 Dec 2021 13:01:07: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:01:15: 23000000 INFO @ Fri, 10 Dec 2021 13:01:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:01:23: 24000000 INFO @ Fri, 10 Dec 2021 13:01:30: 25000000 INFO @ Fri, 10 Dec 2021 13:01:38: 26000000 INFO @ Fri, 10 Dec 2021 13:01:46: 27000000 INFO @ Fri, 10 Dec 2021 13:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.05_summits.bed INFO @ Fri, 10 Dec 2021 13:01:47: Done! pass1 - making usageList (813 chroms): 2 millis pass2 - checking and writing primary data (10293 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:01:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:01:54: 28000000 INFO @ Fri, 10 Dec 2021 13:02:01: 29000000 INFO @ Fri, 10 Dec 2021 13:02:09: 30000000 INFO @ Fri, 10 Dec 2021 13:02:16: 31000000 INFO @ Fri, 10 Dec 2021 13:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:02:24: 32000000 INFO @ Fri, 10 Dec 2021 13:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.10_summits.bed INFO @ Fri, 10 Dec 2021 13:02:24: Done! pass1 - making usageList (712 chroms): 2 millis pass2 - checking and writing primary data (7148 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:02:30: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 13:02:30: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 13:02:30: #1 total tags in treatment: 32689032 INFO @ Fri, 10 Dec 2021 13:02:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:02:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:02:30: #1 tags after filtering in treatment: 32689032 INFO @ Fri, 10 Dec 2021 13:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:02:30: #1 finished! INFO @ Fri, 10 Dec 2021 13:02:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:02:33: #2 number of paired peaks: 380 WARNING @ Fri, 10 Dec 2021 13:02:33: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 10 Dec 2021 13:02:33: start model_add_line... INFO @ Fri, 10 Dec 2021 13:02:34: start X-correlation... INFO @ Fri, 10 Dec 2021 13:02:34: end of X-cor INFO @ Fri, 10 Dec 2021 13:02:34: #2 finished! INFO @ Fri, 10 Dec 2021 13:02:34: #2 predicted fragment length is 133 bps INFO @ Fri, 10 Dec 2021 13:02:34: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 10 Dec 2021 13:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.20_model.r WARNING @ Fri, 10 Dec 2021 13:02:34: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:02:34: #2 You may need to consider one of the other alternative d(s): 4,133 WARNING @ Fri, 10 Dec 2021 13:02:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:02:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:02:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:03:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574277/SRX8574277.20_summits.bed INFO @ Fri, 10 Dec 2021 13:04:20: Done! pass1 - making usageList (579 chroms): 2 millis pass2 - checking and writing primary data (4238 records, 4 fields): 22 millis CompletedMACS2peakCalling