Job ID = 5720838 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:51:34 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 49,722,557 reads read : 49,722,557 reads written : 49,722,557 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: 00:16:01 49722557 reads; of these: 49722557 (100.00%) were unpaired; of these: 3004677 (6.04%) aligned 0 times 34881291 (70.15%) aligned exactly 1 time 11836589 (23.81%) aligned >1 times 93.96% overall alignment rate Time searching: 00:16:01 Overall time: 00:16:01 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 20 files... [bam_rmdupse_core] 12701502 / 46717880 = 0.2719 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 02:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.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 02:39:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:39:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:40:02: 1000000 INFO @ Thu, 16 Apr 2020 02:40:07: 2000000 INFO @ Thu, 16 Apr 2020 02:40:13: 3000000 INFO @ Thu, 16 Apr 2020 02:40:18: 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 02:40:24: 5000000 INFO @ Thu, 16 Apr 2020 02:40:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.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 02:40:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:40:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:40:30: 6000000 INFO @ Thu, 16 Apr 2020 02:40:32: 1000000 INFO @ Thu, 16 Apr 2020 02:40:36: 7000000 INFO @ Thu, 16 Apr 2020 02:40:38: 2000000 INFO @ Thu, 16 Apr 2020 02:40:42: 8000000 INFO @ Thu, 16 Apr 2020 02:40:44: 3000000 INFO @ Thu, 16 Apr 2020 02:40:48: 9000000 INFO @ Thu, 16 Apr 2020 02:40:50: 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 02:40:54: 10000000 INFO @ Thu, 16 Apr 2020 02:40:56: 5000000 INFO @ Thu, 16 Apr 2020 02:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.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 02:40:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:40:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:41:00: 11000000 INFO @ Thu, 16 Apr 2020 02:41:03: 1000000 INFO @ Thu, 16 Apr 2020 02:41:03: 6000000 INFO @ Thu, 16 Apr 2020 02:41:07: 12000000 INFO @ Thu, 16 Apr 2020 02:41:09: 2000000 INFO @ Thu, 16 Apr 2020 02:41:09: 7000000 INFO @ Thu, 16 Apr 2020 02:41:13: 13000000 INFO @ Thu, 16 Apr 2020 02:41:15: 8000000 INFO @ Thu, 16 Apr 2020 02:41:15: 3000000 INFO @ Thu, 16 Apr 2020 02:41:19: 14000000 INFO @ Thu, 16 Apr 2020 02:41:21: 9000000 INFO @ Thu, 16 Apr 2020 02:41:21: 4000000 INFO @ Thu, 16 Apr 2020 02:41:25: 15000000 INFO @ Thu, 16 Apr 2020 02:41:28: 10000000 INFO @ Thu, 16 Apr 2020 02:41:28: 5000000 INFO @ Thu, 16 Apr 2020 02:41:33: 16000000 INFO @ Thu, 16 Apr 2020 02:41:34: 11000000 INFO @ Thu, 16 Apr 2020 02:41:35: 6000000 INFO @ Thu, 16 Apr 2020 02:41:39: 17000000 INFO @ Thu, 16 Apr 2020 02:41:41: 12000000 INFO @ Thu, 16 Apr 2020 02:41:42: 7000000 INFO @ Thu, 16 Apr 2020 02:41:46: 18000000 INFO @ Thu, 16 Apr 2020 02:41:48: 13000000 INFO @ Thu, 16 Apr 2020 02:41:48: 8000000 INFO @ Thu, 16 Apr 2020 02:41:52: 19000000 INFO @ Thu, 16 Apr 2020 02:41:54: 14000000 INFO @ Thu, 16 Apr 2020 02:41:55: 9000000 INFO @ Thu, 16 Apr 2020 02:41:59: 20000000 INFO @ Thu, 16 Apr 2020 02:42:01: 15000000 INFO @ Thu, 16 Apr 2020 02:42:01: 10000000 INFO @ Thu, 16 Apr 2020 02:42:05: 21000000 INFO @ Thu, 16 Apr 2020 02:42:07: 16000000 INFO @ Thu, 16 Apr 2020 02:42:08: 11000000 INFO @ Thu, 16 Apr 2020 02:42:11: 22000000 INFO @ Thu, 16 Apr 2020 02:42:13: 17000000 INFO @ Thu, 16 Apr 2020 02:42:14: 12000000 INFO @ Thu, 16 Apr 2020 02:42:17: 23000000 INFO @ Thu, 16 Apr 2020 02:42:20: 18000000 INFO @ Thu, 16 Apr 2020 02:42:20: 13000000 INFO @ Thu, 16 Apr 2020 02:42:24: 24000000 INFO @ Thu, 16 Apr 2020 02:42:26: 19000000 INFO @ Thu, 16 Apr 2020 02:42:26: 14000000 INFO @ Thu, 16 Apr 2020 02:42:30: 25000000 INFO @ Thu, 16 Apr 2020 02:42:32: 20000000 INFO @ Thu, 16 Apr 2020 02:42:33: 15000000 INFO @ Thu, 16 Apr 2020 02:42:36: 26000000 INFO @ Thu, 16 Apr 2020 02:42:38: 21000000 INFO @ Thu, 16 Apr 2020 02:42:39: 16000000 INFO @ Thu, 16 Apr 2020 02:42:42: 27000000 INFO @ Thu, 16 Apr 2020 02:42:45: 22000000 INFO @ Thu, 16 Apr 2020 02:42:45: 17000000 INFO @ Thu, 16 Apr 2020 02:42:49: 28000000 INFO @ Thu, 16 Apr 2020 02:42:51: 23000000 INFO @ Thu, 16 Apr 2020 02:42:51: 18000000 INFO @ Thu, 16 Apr 2020 02:42:55: 29000000 INFO @ Thu, 16 Apr 2020 02:42:57: 24000000 INFO @ Thu, 16 Apr 2020 02:42:58: 19000000 INFO @ Thu, 16 Apr 2020 02:43:01: 30000000 INFO @ Thu, 16 Apr 2020 02:43:04: 25000000 INFO @ Thu, 16 Apr 2020 02:43:04: 20000000 INFO @ Thu, 16 Apr 2020 02:43:07: 31000000 INFO @ Thu, 16 Apr 2020 02:43:10: 26000000 INFO @ Thu, 16 Apr 2020 02:43:10: 21000000 INFO @ Thu, 16 Apr 2020 02:43:14: 32000000 INFO @ Thu, 16 Apr 2020 02:43:16: 27000000 INFO @ Thu, 16 Apr 2020 02:43:16: 22000000 INFO @ Thu, 16 Apr 2020 02:43:20: 33000000 INFO @ Thu, 16 Apr 2020 02:43:23: 23000000 INFO @ Thu, 16 Apr 2020 02:43:23: 28000000 INFO @ Thu, 16 Apr 2020 02:43:26: 34000000 INFO @ Thu, 16 Apr 2020 02:43:26: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:43:26: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:43:26: #1 total tags in treatment: 34016378 INFO @ Thu, 16 Apr 2020 02:43:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:43:26: #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 02:43:27: #1 tags after filtering in treatment: 34016378 INFO @ Thu, 16 Apr 2020 02:43:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:43:27: #1 finished! INFO @ Thu, 16 Apr 2020 02:43:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:43:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:43:29: #2 number of paired peaks: 209 WARNING @ Thu, 16 Apr 2020 02:43:29: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Thu, 16 Apr 2020 02:43:29: start model_add_line... INFO @ Thu, 16 Apr 2020 02:43:29: 24000000 INFO @ Thu, 16 Apr 2020 02:43:29: start X-correlation... INFO @ Thu, 16 Apr 2020 02:43:29: end of X-cor INFO @ Thu, 16 Apr 2020 02:43:29: #2 finished! INFO @ Thu, 16 Apr 2020 02:43:29: #2 predicted fragment length is 100 bps INFO @ Thu, 16 Apr 2020 02:43:29: #2 alternative fragment length(s) may be 4,88,100 bps INFO @ Thu, 16 Apr 2020 02:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.05_model.r WARNING @ Thu, 16 Apr 2020 02:43:29: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:43:29: #2 You may need to consider one of the other alternative d(s): 4,88,100 WARNING @ Thu, 16 Apr 2020 02:43:29: #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 02:43:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:43:29: 29000000 INFO @ Thu, 16 Apr 2020 02:43:35: 25000000 INFO @ Thu, 16 Apr 2020 02:43:36: 30000000 INFO @ Thu, 16 Apr 2020 02:43:42: 26000000 INFO @ Thu, 16 Apr 2020 02:43:42: 31000000 INFO @ Thu, 16 Apr 2020 02:43:48: 27000000 INFO @ Thu, 16 Apr 2020 02:43:48: 32000000 INFO @ Thu, 16 Apr 2020 02:43:54: 28000000 INFO @ Thu, 16 Apr 2020 02:43:54: 33000000 INFO @ Thu, 16 Apr 2020 02:44:00: 34000000 INFO @ Thu, 16 Apr 2020 02:44:00: 29000000 INFO @ Thu, 16 Apr 2020 02:44:01: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:44:01: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:44:01: #1 total tags in treatment: 34016378 INFO @ Thu, 16 Apr 2020 02:44:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:01: #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 02:44:01: #1 tags after filtering in treatment: 34016378 INFO @ Thu, 16 Apr 2020 02:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:44:01: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:03: #2 number of paired peaks: 209 WARNING @ Thu, 16 Apr 2020 02:44:03: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:03: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:03: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:03: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:03: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:03: #2 predicted fragment length is 100 bps INFO @ Thu, 16 Apr 2020 02:44:03: #2 alternative fragment length(s) may be 4,88,100 bps INFO @ Thu, 16 Apr 2020 02:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.10_model.r WARNING @ Thu, 16 Apr 2020 02:44:03: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:44:03: #2 You may need to consider one of the other alternative d(s): 4,88,100 WARNING @ Thu, 16 Apr 2020 02:44:03: #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 02:44:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:44:06: 30000000 INFO @ Thu, 16 Apr 2020 02:44:12: 31000000 INFO @ Thu, 16 Apr 2020 02:44:18: 32000000 INFO @ Thu, 16 Apr 2020 02:44:23: 33000000 INFO @ Thu, 16 Apr 2020 02:44:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:44:29: 34000000 INFO @ Thu, 16 Apr 2020 02:44:29: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:44:29: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:44:29: #1 total tags in treatment: 34016378 INFO @ Thu, 16 Apr 2020 02:44:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:29: #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 02:44:30: #1 tags after filtering in treatment: 34016378 INFO @ Thu, 16 Apr 2020 02:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:44:30: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:32: #2 number of paired peaks: 209 WARNING @ Thu, 16 Apr 2020 02:44:32: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:32: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:32: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:32: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:32: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:32: #2 predicted fragment length is 100 bps INFO @ Thu, 16 Apr 2020 02:44:32: #2 alternative fragment length(s) may be 4,88,100 bps INFO @ Thu, 16 Apr 2020 02:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.20_model.r WARNING @ Thu, 16 Apr 2020 02:44:32: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:44:32: #2 You may need to consider one of the other alternative d(s): 4,88,100 WARNING @ Thu, 16 Apr 2020 02:44:32: #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 02:44:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.05_summits.bed INFO @ Thu, 16 Apr 2020 02:44:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6162 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:44:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.10_summits.bed INFO @ Thu, 16 Apr 2020 02:45:25: Done! INFO @ Thu, 16 Apr 2020 02:45:29: #3 Call peaks for each chromosome... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3300 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5416213/SRX5416213.20_summits.bed INFO @ Thu, 16 Apr 2020 02:45:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1604 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。