Job ID = 6457497 SRX = SRX4664651 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:38:40 prefetch.2.10.7: 1) Downloading 'SRR7813078'... 2020-06-21T11:38:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:42:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:42:41 prefetch.2.10.7: 1) 'SRR7813078' was downloaded successfully Read 29073741 spots for SRR7813078/SRR7813078.sra Written 29073741 spots for SRR7813078/SRR7813078.sra 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: 00:09:18 29073741 reads; of these: 29073741 (100.00%) were unpaired; of these: 860392 (2.96%) aligned 0 times 18551161 (63.81%) aligned exactly 1 time 9662188 (33.23%) aligned >1 times 97.04% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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 12 files... [bam_rmdupse_core] 5111323 / 28213349 = 0.1812 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 @ Sun, 21 Jun 2020 20:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.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 @ Sun, 21 Jun 2020 20:59:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:59:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:05: 1000000 INFO @ Sun, 21 Jun 2020 20:59:10: 2000000 INFO @ Sun, 21 Jun 2020 20:59:15: 3000000 INFO @ Sun, 21 Jun 2020 20:59:20: 4000000 INFO @ Sun, 21 Jun 2020 20:59:25: 5000000 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 @ Sun, 21 Jun 2020 20:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.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 @ Sun, 21 Jun 2020 20:59:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:59:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:31: 6000000 INFO @ Sun, 21 Jun 2020 20:59:35: 1000000 INFO @ Sun, 21 Jun 2020 20:59:36: 7000000 INFO @ Sun, 21 Jun 2020 20:59:41: 2000000 INFO @ Sun, 21 Jun 2020 20:59:42: 8000000 INFO @ Sun, 21 Jun 2020 20:59:47: 3000000 INFO @ Sun, 21 Jun 2020 20:59:47: 9000000 INFO @ Sun, 21 Jun 2020 20:59:52: 4000000 INFO @ Sun, 21 Jun 2020 20:59:53: 10000000 INFO @ Sun, 21 Jun 2020 20:59:58: 5000000 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 @ Sun, 21 Jun 2020 20:59:59: 11000000 INFO @ Sun, 21 Jun 2020 21:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.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 @ Sun, 21 Jun 2020 21:00:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:03: 6000000 INFO @ Sun, 21 Jun 2020 21:00:04: 12000000 INFO @ Sun, 21 Jun 2020 21:00:06: 1000000 INFO @ Sun, 21 Jun 2020 21:00:09: 7000000 INFO @ Sun, 21 Jun 2020 21:00:10: 13000000 INFO @ Sun, 21 Jun 2020 21:00:11: 2000000 INFO @ Sun, 21 Jun 2020 21:00:15: 8000000 INFO @ Sun, 21 Jun 2020 21:00:16: 14000000 INFO @ Sun, 21 Jun 2020 21:00:17: 3000000 INFO @ Sun, 21 Jun 2020 21:00:21: 9000000 INFO @ Sun, 21 Jun 2020 21:00:22: 15000000 INFO @ Sun, 21 Jun 2020 21:00:23: 4000000 INFO @ Sun, 21 Jun 2020 21:00:26: 10000000 INFO @ Sun, 21 Jun 2020 21:00:27: 16000000 INFO @ Sun, 21 Jun 2020 21:00:28: 5000000 INFO @ Sun, 21 Jun 2020 21:00:32: 11000000 INFO @ Sun, 21 Jun 2020 21:00:33: 17000000 INFO @ Sun, 21 Jun 2020 21:00:34: 6000000 INFO @ Sun, 21 Jun 2020 21:00:38: 12000000 INFO @ Sun, 21 Jun 2020 21:00:39: 18000000 INFO @ Sun, 21 Jun 2020 21:00:40: 7000000 INFO @ Sun, 21 Jun 2020 21:00:44: 13000000 INFO @ Sun, 21 Jun 2020 21:00:44: 19000000 INFO @ Sun, 21 Jun 2020 21:00:45: 8000000 INFO @ Sun, 21 Jun 2020 21:00:49: 14000000 INFO @ Sun, 21 Jun 2020 21:00:50: 20000000 INFO @ Sun, 21 Jun 2020 21:00:51: 9000000 INFO @ Sun, 21 Jun 2020 21:00:55: 15000000 INFO @ Sun, 21 Jun 2020 21:00:56: 21000000 INFO @ Sun, 21 Jun 2020 21:00:57: 10000000 INFO @ Sun, 21 Jun 2020 21:01:00: 16000000 INFO @ Sun, 21 Jun 2020 21:01:02: 22000000 INFO @ Sun, 21 Jun 2020 21:01:03: 11000000 INFO @ Sun, 21 Jun 2020 21:01:06: 17000000 INFO @ Sun, 21 Jun 2020 21:01:08: 23000000 INFO @ Sun, 21 Jun 2020 21:01:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:01:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:01:08: #1 total tags in treatment: 23102026 INFO @ Sun, 21 Jun 2020 21:01:08: 12000000 INFO @ Sun, 21 Jun 2020 21:01:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:01:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:01:09: #1 tags after filtering in treatment: 23101975 INFO @ Sun, 21 Jun 2020 21:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:01:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:01:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:01:10: #2 number of paired peaks: 1023 INFO @ Sun, 21 Jun 2020 21:01:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:01:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:01:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:01:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:01:11: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:01:11: #2 alternative fragment length(s) may be 1,50 bps INFO @ Sun, 21 Jun 2020 21:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.05_model.r WARNING @ Sun, 21 Jun 2020 21:01:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:01:11: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Sun, 21 Jun 2020 21:01:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:01:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:01:12: 18000000 INFO @ Sun, 21 Jun 2020 21:01:14: 13000000 INFO @ Sun, 21 Jun 2020 21:01:18: 19000000 INFO @ Sun, 21 Jun 2020 21:01:20: 14000000 INFO @ Sun, 21 Jun 2020 21:01:24: 20000000 INFO @ Sun, 21 Jun 2020 21:01:25: 15000000 INFO @ Sun, 21 Jun 2020 21:01:29: 21000000 INFO @ Sun, 21 Jun 2020 21:01:31: 16000000 INFO @ Sun, 21 Jun 2020 21:01:35: 22000000 INFO @ Sun, 21 Jun 2020 21:01:36: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:01:41: 23000000 INFO @ Sun, 21 Jun 2020 21:01:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:01:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:01:42: #1 total tags in treatment: 23102026 INFO @ Sun, 21 Jun 2020 21:01:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:01:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:01:42: 18000000 INFO @ Sun, 21 Jun 2020 21:01:42: #1 tags after filtering in treatment: 23101975 INFO @ Sun, 21 Jun 2020 21:01:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:01:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:01:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:01:44: #2 number of paired peaks: 1023 INFO @ Sun, 21 Jun 2020 21:01:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:01:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:01:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:01:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:01:44: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:01:44: #2 alternative fragment length(s) may be 1,50 bps INFO @ Sun, 21 Jun 2020 21:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.10_model.r WARNING @ Sun, 21 Jun 2020 21:01:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:01:44: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Sun, 21 Jun 2020 21:01:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:01:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:01:48: 19000000 INFO @ Sun, 21 Jun 2020 21:01:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:01:54: 20000000 INFO @ Sun, 21 Jun 2020 21:01:59: 21000000 INFO @ Sun, 21 Jun 2020 21:02:05: 22000000 INFO @ Sun, 21 Jun 2020 21:02:10: 23000000 INFO @ Sun, 21 Jun 2020 21:02:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:02:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:02:11: #1 total tags in treatment: 23102026 INFO @ Sun, 21 Jun 2020 21:02:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.05_summits.bed INFO @ Sun, 21 Jun 2020 21:02:11: Done! pass1 - making usageList (614 chroms): 2 millis pass2 - checking and writing primary data (3583 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:02:11: #1 tags after filtering in treatment: 23101975 INFO @ Sun, 21 Jun 2020 21:02:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:13: #2 number of paired peaks: 1023 INFO @ Sun, 21 Jun 2020 21:02:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:13: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:02:13: #2 alternative fragment length(s) may be 1,50 bps INFO @ Sun, 21 Jun 2020 21:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.20_model.r WARNING @ Sun, 21 Jun 2020 21:02:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:02:13: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Sun, 21 Jun 2020 21:02:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:02:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.10_summits.bed INFO @ Sun, 21 Jun 2020 21:02:46: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (2313 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:02:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664651/SRX4664651.20_summits.bed INFO @ Sun, 21 Jun 2020 21:03:14: Done! pass1 - making usageList (419 chroms): 1 millis pass2 - checking and writing primary data (1222 records, 4 fields): 12 millis CompletedMACS2peakCalling