Job ID = 5721096 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 49,577,528 reads read : 99,155,056 reads written : 49,577,528 reads 0-length : 49,577,528 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: 00:19:36 49577528 reads; of these: 49577528 (100.00%) were unpaired; of these: 11470424 (23.14%) aligned 0 times 25561705 (51.56%) aligned exactly 1 time 12545399 (25.30%) aligned >1 times 76.86% overall alignment rate Time searching: 00:19:36 Overall time: 00:19:36 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] 14346207 / 38107104 = 0.3765 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 05:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.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 05:19:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:19:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:19:11: 1000000 INFO @ Thu, 16 Apr 2020 05:19:17: 2000000 INFO @ Thu, 16 Apr 2020 05:19:24: 3000000 INFO @ Thu, 16 Apr 2020 05:19:30: 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 05:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.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 05:19:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:19:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:19:36: 5000000 INFO @ Thu, 16 Apr 2020 05:19:41: 1000000 INFO @ Thu, 16 Apr 2020 05:19:43: 6000000 INFO @ Thu, 16 Apr 2020 05:19:48: 2000000 INFO @ Thu, 16 Apr 2020 05:19:49: 7000000 INFO @ Thu, 16 Apr 2020 05:19:55: 3000000 INFO @ Thu, 16 Apr 2020 05:19:56: 8000000 INFO @ Thu, 16 Apr 2020 05:20:02: 4000000 INFO @ Thu, 16 Apr 2020 05:20:03: 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 @ Thu, 16 Apr 2020 05:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.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 05:20:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:09: 5000000 INFO @ Thu, 16 Apr 2020 05:20:09: 10000000 INFO @ Thu, 16 Apr 2020 05:20:12: 1000000 INFO @ Thu, 16 Apr 2020 05:20:15: 6000000 INFO @ Thu, 16 Apr 2020 05:20:16: 11000000 INFO @ Thu, 16 Apr 2020 05:20:19: 2000000 INFO @ Thu, 16 Apr 2020 05:20:22: 7000000 INFO @ Thu, 16 Apr 2020 05:20:23: 12000000 INFO @ Thu, 16 Apr 2020 05:20:26: 3000000 INFO @ Thu, 16 Apr 2020 05:20:29: 8000000 INFO @ Thu, 16 Apr 2020 05:20:30: 13000000 INFO @ Thu, 16 Apr 2020 05:20:33: 4000000 INFO @ Thu, 16 Apr 2020 05:20:36: 9000000 INFO @ Thu, 16 Apr 2020 05:20:36: 14000000 INFO @ Thu, 16 Apr 2020 05:20:39: 5000000 INFO @ Thu, 16 Apr 2020 05:20:43: 10000000 INFO @ Thu, 16 Apr 2020 05:20:43: 15000000 INFO @ Thu, 16 Apr 2020 05:20:46: 6000000 INFO @ Thu, 16 Apr 2020 05:20:49: 11000000 INFO @ Thu, 16 Apr 2020 05:20:50: 16000000 INFO @ Thu, 16 Apr 2020 05:20:53: 7000000 INFO @ Thu, 16 Apr 2020 05:20:56: 12000000 INFO @ Thu, 16 Apr 2020 05:20:57: 17000000 INFO @ Thu, 16 Apr 2020 05:21:00: 8000000 INFO @ Thu, 16 Apr 2020 05:21:03: 13000000 INFO @ Thu, 16 Apr 2020 05:21:04: 18000000 INFO @ Thu, 16 Apr 2020 05:21:07: 9000000 INFO @ Thu, 16 Apr 2020 05:21:10: 14000000 INFO @ Thu, 16 Apr 2020 05:21:10: 19000000 INFO @ Thu, 16 Apr 2020 05:21:13: 10000000 INFO @ Thu, 16 Apr 2020 05:21:17: 20000000 INFO @ Thu, 16 Apr 2020 05:21:17: 15000000 INFO @ Thu, 16 Apr 2020 05:21:20: 11000000 INFO @ Thu, 16 Apr 2020 05:21:24: 21000000 INFO @ Thu, 16 Apr 2020 05:21:24: 16000000 INFO @ Thu, 16 Apr 2020 05:21:27: 12000000 INFO @ Thu, 16 Apr 2020 05:21:31: 22000000 INFO @ Thu, 16 Apr 2020 05:21:31: 17000000 INFO @ Thu, 16 Apr 2020 05:21:34: 13000000 INFO @ Thu, 16 Apr 2020 05:21:38: 23000000 INFO @ Thu, 16 Apr 2020 05:21:38: 18000000 INFO @ Thu, 16 Apr 2020 05:21:41: 14000000 INFO @ Thu, 16 Apr 2020 05:21:43: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:21:43: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:21:43: #1 total tags in treatment: 23760897 INFO @ Thu, 16 Apr 2020 05:21:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:43: #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 05:21:43: #1 tags after filtering in treatment: 23760897 INFO @ Thu, 16 Apr 2020 05:21:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:21:43: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:45: #2 number of paired peaks: 1236 INFO @ Thu, 16 Apr 2020 05:21:45: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:45: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:45: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:45: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:45: #2 predicted fragment length is 66 bps INFO @ Thu, 16 Apr 2020 05:21:45: #2 alternative fragment length(s) may be 2,66,580,598 bps INFO @ Thu, 16 Apr 2020 05:21:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.05_model.r WARNING @ Thu, 16 Apr 2020 05:21:45: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:21:45: #2 You may need to consider one of the other alternative d(s): 2,66,580,598 WARNING @ Thu, 16 Apr 2020 05:21:45: #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 05:21:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:45: 19000000 INFO @ Thu, 16 Apr 2020 05:21:48: 15000000 INFO @ Thu, 16 Apr 2020 05:21:52: 20000000 INFO @ Thu, 16 Apr 2020 05:21:55: 16000000 INFO @ Thu, 16 Apr 2020 05:21:59: 21000000 INFO @ Thu, 16 Apr 2020 05:22:01: 17000000 INFO @ Thu, 16 Apr 2020 05:22:05: 22000000 INFO @ Thu, 16 Apr 2020 05:22:08: 18000000 INFO @ Thu, 16 Apr 2020 05:22:12: 23000000 INFO @ Thu, 16 Apr 2020 05:22:15: 19000000 INFO @ Thu, 16 Apr 2020 05:22:17: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:22:17: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:22:17: #1 total tags in treatment: 23760897 INFO @ Thu, 16 Apr 2020 05:22:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:17: #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 05:22:18: #1 tags after filtering in treatment: 23760897 INFO @ Thu, 16 Apr 2020 05:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:22:18: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:19: #2 number of paired peaks: 1236 INFO @ Thu, 16 Apr 2020 05:22:19: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:19: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:19: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:19: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:19: #2 predicted fragment length is 66 bps INFO @ Thu, 16 Apr 2020 05:22:19: #2 alternative fragment length(s) may be 2,66,580,598 bps INFO @ Thu, 16 Apr 2020 05:22:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.10_model.r WARNING @ Thu, 16 Apr 2020 05:22:19: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:22:19: #2 You may need to consider one of the other alternative d(s): 2,66,580,598 WARNING @ Thu, 16 Apr 2020 05:22:19: #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 05:22:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:22: 20000000 INFO @ Thu, 16 Apr 2020 05:22:28: 21000000 INFO @ Thu, 16 Apr 2020 05:22:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:34: 22000000 INFO @ Thu, 16 Apr 2020 05:22:41: 23000000 INFO @ Thu, 16 Apr 2020 05:22:45: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:22:45: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:22:45: #1 total tags in treatment: 23760897 INFO @ Thu, 16 Apr 2020 05:22:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:45: #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 05:22:46: #1 tags after filtering in treatment: 23760897 INFO @ Thu, 16 Apr 2020 05:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:22:46: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:47: #2 number of paired peaks: 1236 INFO @ Thu, 16 Apr 2020 05:22:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:48: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:48: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:48: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:48: #2 predicted fragment length is 66 bps INFO @ Thu, 16 Apr 2020 05:22:48: #2 alternative fragment length(s) may be 2,66,580,598 bps INFO @ Thu, 16 Apr 2020 05:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.20_model.r WARNING @ Thu, 16 Apr 2020 05:22:48: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:22:48: #2 You may need to consider one of the other alternative d(s): 2,66,580,598 WARNING @ Thu, 16 Apr 2020 05:22:48: #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 05:22:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.05_summits.bed INFO @ Thu, 16 Apr 2020 05:22:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5340 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:23:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.10_summits.bed INFO @ Thu, 16 Apr 2020 05:23:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3002 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:23:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685750/SRX6685750.20_summits.bed INFO @ Thu, 16 Apr 2020 05:23:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1751 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。