Job ID = 5721095 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 43,050,791 reads read : 86,101,582 reads written : 43,050,791 reads 0-length : 43,050,791 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:16:03 43050791 reads; of these: 43050791 (100.00%) were unpaired; of these: 9812983 (22.79%) aligned 0 times 22375200 (51.97%) aligned exactly 1 time 10862608 (25.23%) aligned >1 times 77.21% overall alignment rate Time searching: 00:16:03 Overall time: 00:16:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11663018 / 33237808 = 0.3509 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 @ Thu, 16 Apr 2020 05:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.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 @ Thu, 16 Apr 2020 05:11:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:11:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:11:15: 1000000 INFO @ Thu, 16 Apr 2020 05:11:20: 2000000 INFO @ Thu, 16 Apr 2020 05:11:26: 3000000 INFO @ Thu, 16 Apr 2020 05:11:32: 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 @ Thu, 16 Apr 2020 05:11:38: 5000000 INFO @ Thu, 16 Apr 2020 05:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.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 @ Thu, 16 Apr 2020 05:11:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:11:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:11:44: 6000000 INFO @ Thu, 16 Apr 2020 05:11:45: 1000000 INFO @ Thu, 16 Apr 2020 05:11:50: 7000000 INFO @ Thu, 16 Apr 2020 05:11:52: 2000000 INFO @ Thu, 16 Apr 2020 05:11:56: 8000000 INFO @ Thu, 16 Apr 2020 05:11:58: 3000000 INFO @ Thu, 16 Apr 2020 05:12:02: 9000000 INFO @ Thu, 16 Apr 2020 05:12:04: 4000000 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 @ Thu, 16 Apr 2020 05:12:08: 10000000 INFO @ Thu, 16 Apr 2020 05:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.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 @ Thu, 16 Apr 2020 05:12:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:12:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:12:11: 5000000 INFO @ Thu, 16 Apr 2020 05:12:15: 11000000 INFO @ Thu, 16 Apr 2020 05:12:15: 1000000 INFO @ Thu, 16 Apr 2020 05:12:17: 6000000 INFO @ Thu, 16 Apr 2020 05:12:21: 12000000 INFO @ Thu, 16 Apr 2020 05:12:22: 2000000 INFO @ Thu, 16 Apr 2020 05:12:24: 7000000 INFO @ Thu, 16 Apr 2020 05:12:28: 13000000 INFO @ Thu, 16 Apr 2020 05:12:29: 3000000 INFO @ Thu, 16 Apr 2020 05:12:30: 8000000 INFO @ Thu, 16 Apr 2020 05:12:34: 14000000 INFO @ Thu, 16 Apr 2020 05:12:35: 4000000 INFO @ Thu, 16 Apr 2020 05:12:36: 9000000 INFO @ Thu, 16 Apr 2020 05:12:40: 15000000 INFO @ Thu, 16 Apr 2020 05:12:42: 5000000 INFO @ Thu, 16 Apr 2020 05:12:43: 10000000 INFO @ Thu, 16 Apr 2020 05:12:46: 16000000 INFO @ Thu, 16 Apr 2020 05:12:48: 6000000 INFO @ Thu, 16 Apr 2020 05:12:49: 11000000 INFO @ Thu, 16 Apr 2020 05:12:53: 17000000 INFO @ Thu, 16 Apr 2020 05:12:55: 7000000 INFO @ Thu, 16 Apr 2020 05:12:56: 12000000 INFO @ Thu, 16 Apr 2020 05:12:59: 18000000 INFO @ Thu, 16 Apr 2020 05:13:01: 8000000 INFO @ Thu, 16 Apr 2020 05:13:02: 13000000 INFO @ Thu, 16 Apr 2020 05:13:05: 19000000 INFO @ Thu, 16 Apr 2020 05:13:07: 9000000 INFO @ Thu, 16 Apr 2020 05:13:08: 14000000 INFO @ Thu, 16 Apr 2020 05:13:12: 20000000 INFO @ Thu, 16 Apr 2020 05:13:14: 10000000 INFO @ Thu, 16 Apr 2020 05:13:15: 15000000 INFO @ Thu, 16 Apr 2020 05:13:18: 21000000 INFO @ Thu, 16 Apr 2020 05:13:20: 11000000 INFO @ Thu, 16 Apr 2020 05:13:21: 16000000 INFO @ Thu, 16 Apr 2020 05:13:22: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:13:22: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:13:22: #1 total tags in treatment: 21574790 INFO @ Thu, 16 Apr 2020 05:13:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:13:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:13:22: #1 tags after filtering in treatment: 21574790 INFO @ Thu, 16 Apr 2020 05:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:13:22: #1 finished! INFO @ Thu, 16 Apr 2020 05:13:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:13:24: #2 number of paired peaks: 1409 INFO @ Thu, 16 Apr 2020 05:13:24: start model_add_line... INFO @ Thu, 16 Apr 2020 05:13:24: start X-correlation... INFO @ Thu, 16 Apr 2020 05:13:24: end of X-cor INFO @ Thu, 16 Apr 2020 05:13:24: #2 finished! INFO @ Thu, 16 Apr 2020 05:13:24: #2 predicted fragment length is 76 bps INFO @ Thu, 16 Apr 2020 05:13:24: #2 alternative fragment length(s) may be 3,76 bps INFO @ Thu, 16 Apr 2020 05:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.05_model.r WARNING @ Thu, 16 Apr 2020 05:13:24: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:13:24: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Thu, 16 Apr 2020 05:13:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:13:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:13:27: 12000000 INFO @ Thu, 16 Apr 2020 05:13:28: 17000000 INFO @ Thu, 16 Apr 2020 05:13:33: 13000000 INFO @ Thu, 16 Apr 2020 05:13:34: 18000000 INFO @ Thu, 16 Apr 2020 05:13:39: 14000000 INFO @ Thu, 16 Apr 2020 05:13:40: 19000000 INFO @ Thu, 16 Apr 2020 05:13:46: 15000000 INFO @ Thu, 16 Apr 2020 05:13:47: 20000000 INFO @ Thu, 16 Apr 2020 05:13:52: 16000000 INFO @ Thu, 16 Apr 2020 05:13:53: 21000000 INFO @ Thu, 16 Apr 2020 05:13:57: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:13:57: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:13:57: #1 total tags in treatment: 21574790 INFO @ Thu, 16 Apr 2020 05:13:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:13:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:13:57: #1 tags after filtering in treatment: 21574790 INFO @ Thu, 16 Apr 2020 05:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:13:57: #1 finished! INFO @ Thu, 16 Apr 2020 05:13:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:13:58: 17000000 INFO @ Thu, 16 Apr 2020 05:13:59: #2 number of paired peaks: 1409 INFO @ Thu, 16 Apr 2020 05:13:59: start model_add_line... INFO @ Thu, 16 Apr 2020 05:13:59: start X-correlation... INFO @ Thu, 16 Apr 2020 05:13:59: end of X-cor INFO @ Thu, 16 Apr 2020 05:13:59: #2 finished! INFO @ Thu, 16 Apr 2020 05:13:59: #2 predicted fragment length is 76 bps INFO @ Thu, 16 Apr 2020 05:13:59: #2 alternative fragment length(s) may be 3,76 bps INFO @ Thu, 16 Apr 2020 05:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.10_model.r WARNING @ Thu, 16 Apr 2020 05:13:59: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:13:59: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Thu, 16 Apr 2020 05:13:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:13:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:14:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:14:04: 18000000 INFO @ Thu, 16 Apr 2020 05:14:10: 19000000 INFO @ Thu, 16 Apr 2020 05:14:16: 20000000 INFO @ Thu, 16 Apr 2020 05:14:21: 21000000 INFO @ Thu, 16 Apr 2020 05:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.05_summits.bed INFO @ Thu, 16 Apr 2020 05:14:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5298 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:14:25: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:14:25: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:14:25: #1 total tags in treatment: 21574790 INFO @ Thu, 16 Apr 2020 05:14:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:14:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:14:25: #1 tags after filtering in treatment: 21574790 INFO @ Thu, 16 Apr 2020 05:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:14:25: #1 finished! INFO @ Thu, 16 Apr 2020 05:14:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:14:27: #2 number of paired peaks: 1409 INFO @ Thu, 16 Apr 2020 05:14:27: start model_add_line... INFO @ Thu, 16 Apr 2020 05:14:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:14:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:14:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:14:27: #2 predicted fragment length is 76 bps INFO @ Thu, 16 Apr 2020 05:14:27: #2 alternative fragment length(s) may be 3,76 bps INFO @ Thu, 16 Apr 2020 05:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.20_model.r WARNING @ Thu, 16 Apr 2020 05:14:27: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:14:27: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Thu, 16 Apr 2020 05:14:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:14:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:14:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:15:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.10_summits.bed INFO @ Thu, 16 Apr 2020 05:15:01: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3077 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:15:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685749/SRX6685749.20_summits.bed INFO @ Thu, 16 Apr 2020 05:15:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1895 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。