Job ID = 4288928 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:34:09 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 : 24,346,045 reads read : 48,692,090 reads written : 24,346,045 reads 0-length : 24,346,045 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:53 24346045 reads; of these: 24346045 (100.00%) were unpaired; of these: 1024533 (4.21%) aligned 0 times 17508607 (71.92%) aligned exactly 1 time 5812905 (23.88%) aligned >1 times 95.79% overall alignment rate Time searching: 00:29:56 Overall time: 00:29:57 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 12 files... [bam_rmdupse_core] 1720518 / 23321512 = 0.0738 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.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 @ Tue, 10 Dec 2019 13:42:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:42:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:42:42: 1000000 INFO @ Tue, 10 Dec 2019 13:42:52: 2000000 INFO @ Tue, 10 Dec 2019 13:43:01: 3000000 INFO @ Tue, 10 Dec 2019 13:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.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 @ Tue, 10 Dec 2019 13:43:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:11: 1000000 INFO @ Tue, 10 Dec 2019 13:43:11: 4000000 INFO @ Tue, 10 Dec 2019 13:43:20: 2000000 INFO @ Tue, 10 Dec 2019 13:43:21: 5000000 INFO @ Tue, 10 Dec 2019 13:43:29: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:43:31: 6000000 INFO @ Tue, 10 Dec 2019 13:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.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 @ Tue, 10 Dec 2019 13:43:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:38: 4000000 INFO @ Tue, 10 Dec 2019 13:43:40: 7000000 INFO @ Tue, 10 Dec 2019 13:43:45: 1000000 INFO @ Tue, 10 Dec 2019 13:43:47: 5000000 INFO @ Tue, 10 Dec 2019 13:43:50: 8000000 INFO @ Tue, 10 Dec 2019 13:43:56: 6000000 INFO @ Tue, 10 Dec 2019 13:43:57: 2000000 INFO @ Tue, 10 Dec 2019 13:44:00: 9000000 INFO @ Tue, 10 Dec 2019 13:44:04: 7000000 INFO @ Tue, 10 Dec 2019 13:44:09: 3000000 INFO @ Tue, 10 Dec 2019 13:44:09: 10000000 INFO @ Tue, 10 Dec 2019 13:44:13: 8000000 INFO @ Tue, 10 Dec 2019 13:44:19: 11000000 INFO @ Tue, 10 Dec 2019 13:44:22: 4000000 INFO @ Tue, 10 Dec 2019 13:44:22: 9000000 INFO @ Tue, 10 Dec 2019 13:44:29: 12000000 INFO @ Tue, 10 Dec 2019 13:44:31: 10000000 INFO @ Tue, 10 Dec 2019 13:44:34: 5000000 INFO @ Tue, 10 Dec 2019 13:44:39: 13000000 INFO @ Tue, 10 Dec 2019 13:44:40: 11000000 INFO @ Tue, 10 Dec 2019 13:44:46: 6000000 INFO @ Tue, 10 Dec 2019 13:44:48: 14000000 INFO @ Tue, 10 Dec 2019 13:44:48: 12000000 INFO @ Tue, 10 Dec 2019 13:44:57: 13000000 INFO @ Tue, 10 Dec 2019 13:44:57: 7000000 INFO @ Tue, 10 Dec 2019 13:44:58: 15000000 INFO @ Tue, 10 Dec 2019 13:45:06: 14000000 INFO @ Tue, 10 Dec 2019 13:45:07: 16000000 INFO @ Tue, 10 Dec 2019 13:45:09: 8000000 INFO @ Tue, 10 Dec 2019 13:45:15: 15000000 INFO @ Tue, 10 Dec 2019 13:45:17: 17000000 INFO @ Tue, 10 Dec 2019 13:45:21: 9000000 INFO @ Tue, 10 Dec 2019 13:45:24: 16000000 INFO @ Tue, 10 Dec 2019 13:45:27: 18000000 INFO @ Tue, 10 Dec 2019 13:45:32: 17000000 INFO @ Tue, 10 Dec 2019 13:45:33: 10000000 INFO @ Tue, 10 Dec 2019 13:45:36: 19000000 INFO @ Tue, 10 Dec 2019 13:45:41: 18000000 INFO @ Tue, 10 Dec 2019 13:45:44: 11000000 INFO @ Tue, 10 Dec 2019 13:45:46: 20000000 INFO @ Tue, 10 Dec 2019 13:45:50: 19000000 INFO @ Tue, 10 Dec 2019 13:45:56: 21000000 INFO @ Tue, 10 Dec 2019 13:45:56: 12000000 INFO @ Tue, 10 Dec 2019 13:45:59: 20000000 INFO @ Tue, 10 Dec 2019 13:46:02: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:46:02: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:46:02: #1 total tags in treatment: 21600994 INFO @ Tue, 10 Dec 2019 13:46:02: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:46:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:46:02: #1 tags after filtering in treatment: 21600846 INFO @ Tue, 10 Dec 2019 13:46:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:46:02: #1 finished! INFO @ Tue, 10 Dec 2019 13:46:02: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:46:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:46:05: #2 number of paired peaks: 5082 INFO @ Tue, 10 Dec 2019 13:46:05: start model_add_line... INFO @ Tue, 10 Dec 2019 13:46:05: start X-correlation... INFO @ Tue, 10 Dec 2019 13:46:05: end of X-cor INFO @ Tue, 10 Dec 2019 13:46:05: #2 finished! INFO @ Tue, 10 Dec 2019 13:46:05: #2 predicted fragment length is 83 bps INFO @ Tue, 10 Dec 2019 13:46:05: #2 alternative fragment length(s) may be 83,544 bps INFO @ Tue, 10 Dec 2019 13:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.05_model.r WARNING @ Tue, 10 Dec 2019 13:46:05: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:46:05: #2 You may need to consider one of the other alternative d(s): 83,544 WARNING @ Tue, 10 Dec 2019 13:46:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:46:05: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:46:08: 21000000 INFO @ Tue, 10 Dec 2019 13:46:08: 13000000 INFO @ Tue, 10 Dec 2019 13:46:13: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:46:13: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:46:13: #1 total tags in treatment: 21600994 INFO @ Tue, 10 Dec 2019 13:46:13: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:46:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:46:14: #1 tags after filtering in treatment: 21600846 INFO @ Tue, 10 Dec 2019 13:46:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:46:14: #1 finished! INFO @ Tue, 10 Dec 2019 13:46:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:46:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:46:16: #2 number of paired peaks: 5082 INFO @ Tue, 10 Dec 2019 13:46:16: start model_add_line... INFO @ Tue, 10 Dec 2019 13:46:16: start X-correlation... INFO @ Tue, 10 Dec 2019 13:46:16: end of X-cor INFO @ Tue, 10 Dec 2019 13:46:16: #2 finished! INFO @ Tue, 10 Dec 2019 13:46:16: #2 predicted fragment length is 83 bps INFO @ Tue, 10 Dec 2019 13:46:16: #2 alternative fragment length(s) may be 83,544 bps INFO @ Tue, 10 Dec 2019 13:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.10_model.r WARNING @ Tue, 10 Dec 2019 13:46:16: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:46:16: #2 You may need to consider one of the other alternative d(s): 83,544 WARNING @ Tue, 10 Dec 2019 13:46:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:46:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:46:19: 14000000 INFO @ Tue, 10 Dec 2019 13:46:30: 15000000 INFO @ Tue, 10 Dec 2019 13:46:41: 16000000 INFO @ Tue, 10 Dec 2019 13:46:52: 17000000 INFO @ Tue, 10 Dec 2019 13:47:03: 18000000 INFO @ Tue, 10 Dec 2019 13:47:13: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:47:14: 19000000 INFO @ Tue, 10 Dec 2019 13:47:24: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:47:26: 20000000 INFO @ Tue, 10 Dec 2019 13:47:37: 21000000 INFO @ Tue, 10 Dec 2019 13:47:44: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:47:44: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:47:44: #1 total tags in treatment: 21600994 INFO @ Tue, 10 Dec 2019 13:47:44: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:47:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:47:44: #1 tags after filtering in treatment: 21600846 INFO @ Tue, 10 Dec 2019 13:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:47:44: #1 finished! INFO @ Tue, 10 Dec 2019 13:47:44: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.05_summits.bed INFO @ Tue, 10 Dec 2019 13:47:46: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1151 records, 4 fields): 8 millis INFO @ Tue, 10 Dec 2019 13:47:47: #2 number of paired peaks: 5082 INFO @ Tue, 10 Dec 2019 13:47:47: start model_add_line... CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:47:47: start X-correlation... INFO @ Tue, 10 Dec 2019 13:47:47: end of X-cor INFO @ Tue, 10 Dec 2019 13:47:47: #2 finished! INFO @ Tue, 10 Dec 2019 13:47:47: #2 predicted fragment length is 83 bps INFO @ Tue, 10 Dec 2019 13:47:47: #2 alternative fragment length(s) may be 83,544 bps INFO @ Tue, 10 Dec 2019 13:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.20_model.r WARNING @ Tue, 10 Dec 2019 13:47:47: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:47:47: #2 You may need to consider one of the other alternative d(s): 83,544 WARNING @ Tue, 10 Dec 2019 13:47:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:47:47: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.10_summits.bed INFO @ Tue, 10 Dec 2019 13:47:57: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (650 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:48:55: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460567/SRX5460567.20_summits.bed INFO @ Tue, 10 Dec 2019 13:49:28: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。