Job ID = 1294733 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:46:11 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 ) 2019-06-03T00:46:11 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 ) 2019-06-03T00:46:42 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T00:52:03 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 ) 2019-06-03T00:52:03 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 ) 2019-06-03T00:53:22 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 ) 2019-06-03T00:53:22 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 ) 2019-06-03T00:54:17 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 ) 2019-06-03T00:54:29 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 : 21,862,240 reads read : 21,862,240 reads written : 21,862,240 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:37 21862240 reads; of these: 21862240 (100.00%) were unpaired; of these: 1482759 (6.78%) aligned 0 times 16232003 (74.25%) aligned exactly 1 time 4147478 (18.97%) aligned >1 times 93.22% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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 12 files... [bam_rmdupse_core] 4854124 / 20379481 = 0.2382 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 10:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.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 @ Mon, 03 Jun 2019 10:12:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:12:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.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 @ Mon, 03 Jun 2019 10:12:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:12:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.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 @ Mon, 03 Jun 2019 10:12:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:12:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:12:39: 1000000 INFO @ Mon, 03 Jun 2019 10:12:40: 1000000 INFO @ Mon, 03 Jun 2019 10:12:40: 1000000 INFO @ Mon, 03 Jun 2019 10:12:46: 2000000 INFO @ Mon, 03 Jun 2019 10:12:48: 2000000 INFO @ Mon, 03 Jun 2019 10:12:48: 2000000 INFO @ Mon, 03 Jun 2019 10:12:53: 3000000 INFO @ Mon, 03 Jun 2019 10:12:56: 3000000 INFO @ Mon, 03 Jun 2019 10:12:56: 3000000 INFO @ Mon, 03 Jun 2019 10:13:01: 4000000 INFO @ Mon, 03 Jun 2019 10:13:04: 4000000 INFO @ Mon, 03 Jun 2019 10:13:04: 4000000 INFO @ Mon, 03 Jun 2019 10:13:08: 5000000 INFO @ Mon, 03 Jun 2019 10:13:12: 5000000 INFO @ Mon, 03 Jun 2019 10:13:12: 5000000 INFO @ Mon, 03 Jun 2019 10:13:15: 6000000 INFO @ Mon, 03 Jun 2019 10:13:20: 6000000 INFO @ Mon, 03 Jun 2019 10:13:20: 6000000 INFO @ Mon, 03 Jun 2019 10:13:23: 7000000 INFO @ Mon, 03 Jun 2019 10:13:28: 7000000 INFO @ Mon, 03 Jun 2019 10:13:28: 7000000 INFO @ Mon, 03 Jun 2019 10:13:30: 8000000 INFO @ Mon, 03 Jun 2019 10:13:36: 8000000 INFO @ Mon, 03 Jun 2019 10:13:36: 8000000 INFO @ Mon, 03 Jun 2019 10:13:37: 9000000 INFO @ Mon, 03 Jun 2019 10:13:44: 9000000 INFO @ Mon, 03 Jun 2019 10:13:45: 9000000 INFO @ Mon, 03 Jun 2019 10:13:45: 10000000 INFO @ Mon, 03 Jun 2019 10:13:52: 11000000 INFO @ Mon, 03 Jun 2019 10:13:52: 10000000 INFO @ Mon, 03 Jun 2019 10:13:53: 10000000 INFO @ Mon, 03 Jun 2019 10:13:59: 12000000 INFO @ Mon, 03 Jun 2019 10:14:00: 11000000 INFO @ Mon, 03 Jun 2019 10:14:01: 11000000 INFO @ Mon, 03 Jun 2019 10:14:07: 13000000 INFO @ Mon, 03 Jun 2019 10:14:08: 12000000 INFO @ Mon, 03 Jun 2019 10:14:09: 12000000 INFO @ Mon, 03 Jun 2019 10:14:14: 14000000 INFO @ Mon, 03 Jun 2019 10:14:16: 13000000 INFO @ Mon, 03 Jun 2019 10:14:17: 13000000 INFO @ Mon, 03 Jun 2019 10:14:21: 15000000 INFO @ Mon, 03 Jun 2019 10:14:24: 14000000 INFO @ Mon, 03 Jun 2019 10:14:25: 14000000 INFO @ Mon, 03 Jun 2019 10:14:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:14:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:14:25: #1 total tags in treatment: 15525357 INFO @ Mon, 03 Jun 2019 10:14:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:14:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:14:25: #1 tags after filtering in treatment: 15525357 INFO @ Mon, 03 Jun 2019 10:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:14:25: #1 finished! INFO @ Mon, 03 Jun 2019 10:14:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:14:27: #2 number of paired peaks: 428 WARNING @ Mon, 03 Jun 2019 10:14:27: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Mon, 03 Jun 2019 10:14:27: start model_add_line... INFO @ Mon, 03 Jun 2019 10:14:27: start X-correlation... INFO @ Mon, 03 Jun 2019 10:14:27: end of X-cor INFO @ Mon, 03 Jun 2019 10:14:27: #2 finished! INFO @ Mon, 03 Jun 2019 10:14:27: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 10:14:27: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 10:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.05_model.r INFO @ Mon, 03 Jun 2019 10:14:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:14:32: 15000000 INFO @ Mon, 03 Jun 2019 10:14:33: 15000000 INFO @ Mon, 03 Jun 2019 10:14:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:14:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:14:36: #1 total tags in treatment: 15525357 INFO @ Mon, 03 Jun 2019 10:14:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:14:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:14:36: #1 tags after filtering in treatment: 15525357 INFO @ Mon, 03 Jun 2019 10:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:14:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:14:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:14:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:14:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:14:37: #1 total tags in treatment: 15525357 INFO @ Mon, 03 Jun 2019 10:14:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:14:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:14:38: #1 tags after filtering in treatment: 15525357 INFO @ Mon, 03 Jun 2019 10:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:14:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:14:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:14:38: #2 number of paired peaks: 428 WARNING @ Mon, 03 Jun 2019 10:14:38: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Mon, 03 Jun 2019 10:14:38: start model_add_line... INFO @ Mon, 03 Jun 2019 10:14:38: start X-correlation... INFO @ Mon, 03 Jun 2019 10:14:38: end of X-cor INFO @ Mon, 03 Jun 2019 10:14:38: #2 finished! INFO @ Mon, 03 Jun 2019 10:14:38: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 10:14:38: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 10:14:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.20_model.r INFO @ Mon, 03 Jun 2019 10:14:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:14:39: #2 number of paired peaks: 428 WARNING @ Mon, 03 Jun 2019 10:14:39: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Mon, 03 Jun 2019 10:14:39: start model_add_line... INFO @ Mon, 03 Jun 2019 10:14:39: start X-correlation... INFO @ Mon, 03 Jun 2019 10:14:39: end of X-cor INFO @ Mon, 03 Jun 2019 10:14:39: #2 finished! INFO @ Mon, 03 Jun 2019 10:14:39: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 10:14:39: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 10:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.10_model.r INFO @ Mon, 03 Jun 2019 10:14:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:15:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:15:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:15:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.05_summits.bed INFO @ Mon, 03 Jun 2019 10:15:34: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7383 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:15:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.20_summits.bed INFO @ Mon, 03 Jun 2019 10:15:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3392 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287847/SRX287847.10_summits.bed INFO @ Mon, 03 Jun 2019 10:15:47: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5596 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。