Job ID = 2640419 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:45:13 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 36,957,287 reads read : 36,957,287 reads written : 36,957,287 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:04 36957287 reads; of these: 36957287 (100.00%) were unpaired; of these: 12002100 (32.48%) aligned 0 times 17150074 (46.41%) aligned exactly 1 time 7805113 (21.12%) aligned >1 times 67.52% overall alignment rate Time searching: 00:18:05 Overall time: 00:18:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 14646552 / 24955187 = 0.5869 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:11:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:11:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:11:14: 1000000 INFO @ Sat, 24 Aug 2019 17:11:21: 2000000 INFO @ Sat, 24 Aug 2019 17:11:28: 3000000 INFO @ Sat, 24 Aug 2019 17:11:35: 4000000 INFO @ Sat, 24 Aug 2019 17:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:11:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:11:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:11:42: 5000000 INFO @ Sat, 24 Aug 2019 17:11:43: 1000000 INFO @ Sat, 24 Aug 2019 17:11:49: 6000000 INFO @ Sat, 24 Aug 2019 17:11:50: 2000000 INFO @ Sat, 24 Aug 2019 17:11:55: 7000000 INFO @ Sat, 24 Aug 2019 17:11:57: 3000000 INFO @ Sat, 24 Aug 2019 17:12:02: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:12:04: 4000000 INFO @ Sat, 24 Aug 2019 17:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:12:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:12:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:12:09: 9000000 INFO @ Sat, 24 Aug 2019 17:12:10: 5000000 INFO @ Sat, 24 Aug 2019 17:12:13: 1000000 INFO @ Sat, 24 Aug 2019 17:12:16: 10000000 INFO @ Sat, 24 Aug 2019 17:12:17: 6000000 INFO @ Sat, 24 Aug 2019 17:12:19: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:12:19: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:12:19: #1 total tags in treatment: 10308635 INFO @ Sat, 24 Aug 2019 17:12:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:12:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:12:19: #1 tags after filtering in treatment: 10308498 INFO @ Sat, 24 Aug 2019 17:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:12:19: #1 finished! INFO @ Sat, 24 Aug 2019 17:12:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:12:20: 2000000 INFO @ Sat, 24 Aug 2019 17:12:22: #2 number of paired peaks: 32943 INFO @ Sat, 24 Aug 2019 17:12:22: start model_add_line... INFO @ Sat, 24 Aug 2019 17:12:22: start X-correlation... INFO @ Sat, 24 Aug 2019 17:12:22: end of X-cor INFO @ Sat, 24 Aug 2019 17:12:22: #2 finished! INFO @ Sat, 24 Aug 2019 17:12:22: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 17:12:22: #2 alternative fragment length(s) may be 42,109 bps INFO @ Sat, 24 Aug 2019 17:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.05_model.r WARNING @ Sat, 24 Aug 2019 17:12:22: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:12:22: #2 You may need to consider one of the other alternative d(s): 42,109 WARNING @ Sat, 24 Aug 2019 17:12:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:12:22: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:12:24: 7000000 INFO @ Sat, 24 Aug 2019 17:12:27: 3000000 INFO @ Sat, 24 Aug 2019 17:12:31: 8000000 INFO @ Sat, 24 Aug 2019 17:12:34: 4000000 INFO @ Sat, 24 Aug 2019 17:12:38: 9000000 INFO @ Sat, 24 Aug 2019 17:12:41: 5000000 INFO @ Sat, 24 Aug 2019 17:12:45: 10000000 INFO @ Sat, 24 Aug 2019 17:12:47: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:12:47: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:12:47: #1 total tags in treatment: 10308635 INFO @ Sat, 24 Aug 2019 17:12:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:12:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:12:47: #1 tags after filtering in treatment: 10308498 INFO @ Sat, 24 Aug 2019 17:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:12:47: #1 finished! INFO @ Sat, 24 Aug 2019 17:12:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:12:48: 6000000 INFO @ Sat, 24 Aug 2019 17:12:50: #2 number of paired peaks: 32943 INFO @ Sat, 24 Aug 2019 17:12:50: start model_add_line... INFO @ Sat, 24 Aug 2019 17:12:50: start X-correlation... INFO @ Sat, 24 Aug 2019 17:12:50: end of X-cor INFO @ Sat, 24 Aug 2019 17:12:50: #2 finished! INFO @ Sat, 24 Aug 2019 17:12:50: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 17:12:50: #2 alternative fragment length(s) may be 42,109 bps INFO @ Sat, 24 Aug 2019 17:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.10_model.r WARNING @ Sat, 24 Aug 2019 17:12:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:12:50: #2 You may need to consider one of the other alternative d(s): 42,109 WARNING @ Sat, 24 Aug 2019 17:12:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:12:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:12:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:12:54: 7000000 INFO @ Sat, 24 Aug 2019 17:13:01: 8000000 INFO @ Sat, 24 Aug 2019 17:13:08: 9000000 INFO @ Sat, 24 Aug 2019 17:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.05_summits.bed INFO @ Sat, 24 Aug 2019 17:13:11: Done! pass1 - making usageList (81 chroms): 3 millis pass2 - checking and writing primary data (2927 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:13:15: 10000000 INFO @ Sat, 24 Aug 2019 17:13:17: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:13:17: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:13:17: #1 total tags in treatment: 10308635 INFO @ Sat, 24 Aug 2019 17:13:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:13:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:13:18: #1 tags after filtering in treatment: 10308498 INFO @ Sat, 24 Aug 2019 17:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:13:18: #1 finished! INFO @ Sat, 24 Aug 2019 17:13:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:13:20: #2 number of paired peaks: 32943 INFO @ Sat, 24 Aug 2019 17:13:20: start model_add_line... INFO @ Sat, 24 Aug 2019 17:13:21: start X-correlation... INFO @ Sat, 24 Aug 2019 17:13:21: end of X-cor INFO @ Sat, 24 Aug 2019 17:13:21: #2 finished! INFO @ Sat, 24 Aug 2019 17:13:21: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 17:13:21: #2 alternative fragment length(s) may be 42,109 bps INFO @ Sat, 24 Aug 2019 17:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.20_model.r WARNING @ Sat, 24 Aug 2019 17:13:21: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:13:21: #2 You may need to consider one of the other alternative d(s): 42,109 WARNING @ Sat, 24 Aug 2019 17:13:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:13:21: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:13:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.10_summits.bed INFO @ Sat, 24 Aug 2019 17:13:39: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (1344 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:13:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208969/SRX208969.20_summits.bed INFO @ Sat, 24 Aug 2019 17:14:09: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (532 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。