Job ID = 1294595 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:11:13 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 : NET - Reading information from the socket failed ) 1900-01-00T00:00:00 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 : NET - Reading information from the socket failed ) 2019-06-03T00:11:13 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 ) 2019-06-03T00:12:45 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 ) 2019-06-03T00:12:45 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 : 19,172,712 reads read : 19,172,712 reads written : 19,172,712 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: 00:05:56 19172712 reads; of these: 19172712 (100.00%) were unpaired; of these: 990552 (5.17%) aligned 0 times 16377540 (85.42%) aligned exactly 1 time 1804620 (9.41%) aligned >1 times 94.83% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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 8 files... [bam_rmdupse_core] 2395058 / 18182160 = 0.1317 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 09:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.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 09:30:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:30:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.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 09:30:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:30:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.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 09:30:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:30:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:02: 1000000 INFO @ Mon, 03 Jun 2019 09:31:03: 1000000 INFO @ Mon, 03 Jun 2019 09:31:04: 1000000 INFO @ Mon, 03 Jun 2019 09:31:10: 2000000 INFO @ Mon, 03 Jun 2019 09:31:11: 2000000 INFO @ Mon, 03 Jun 2019 09:31:14: 2000000 INFO @ Mon, 03 Jun 2019 09:31:17: 3000000 INFO @ Mon, 03 Jun 2019 09:31:18: 3000000 INFO @ Mon, 03 Jun 2019 09:31:24: 4000000 INFO @ Mon, 03 Jun 2019 09:31:24: 3000000 INFO @ Mon, 03 Jun 2019 09:31:26: 4000000 INFO @ Mon, 03 Jun 2019 09:31:31: 5000000 INFO @ Mon, 03 Jun 2019 09:31:34: 4000000 INFO @ Mon, 03 Jun 2019 09:31:34: 5000000 INFO @ Mon, 03 Jun 2019 09:31:39: 6000000 INFO @ Mon, 03 Jun 2019 09:31:42: 6000000 INFO @ Mon, 03 Jun 2019 09:31:43: 5000000 INFO @ Mon, 03 Jun 2019 09:31:46: 7000000 INFO @ Mon, 03 Jun 2019 09:31:50: 7000000 INFO @ Mon, 03 Jun 2019 09:31:53: 6000000 INFO @ Mon, 03 Jun 2019 09:31:53: 8000000 INFO @ Mon, 03 Jun 2019 09:31:57: 8000000 INFO @ Mon, 03 Jun 2019 09:32:01: 9000000 INFO @ Mon, 03 Jun 2019 09:32:02: 7000000 INFO @ Mon, 03 Jun 2019 09:32:05: 9000000 INFO @ Mon, 03 Jun 2019 09:32:08: 10000000 INFO @ Mon, 03 Jun 2019 09:32:11: 8000000 INFO @ Mon, 03 Jun 2019 09:32:13: 10000000 INFO @ Mon, 03 Jun 2019 09:32:15: 11000000 INFO @ Mon, 03 Jun 2019 09:32:21: 11000000 INFO @ Mon, 03 Jun 2019 09:32:21: 9000000 INFO @ Mon, 03 Jun 2019 09:32:23: 12000000 INFO @ Mon, 03 Jun 2019 09:32:29: 12000000 INFO @ Mon, 03 Jun 2019 09:32:30: 13000000 INFO @ Mon, 03 Jun 2019 09:32:31: 10000000 INFO @ Mon, 03 Jun 2019 09:32:36: 13000000 INFO @ Mon, 03 Jun 2019 09:32:37: 14000000 INFO @ Mon, 03 Jun 2019 09:32:40: 11000000 INFO @ Mon, 03 Jun 2019 09:32:44: 14000000 INFO @ Mon, 03 Jun 2019 09:32:44: 15000000 INFO @ Mon, 03 Jun 2019 09:32:50: 12000000 INFO @ Mon, 03 Jun 2019 09:32:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:32:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:32:50: #1 total tags in treatment: 15787102 INFO @ Mon, 03 Jun 2019 09:32:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:32:50: #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 09:32:51: #1 tags after filtering in treatment: 15787102 INFO @ Mon, 03 Jun 2019 09:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:32:51: #1 finished! INFO @ Mon, 03 Jun 2019 09:32:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:32:52: 15000000 INFO @ Mon, 03 Jun 2019 09:32:52: #2 number of paired peaks: 1582 INFO @ Mon, 03 Jun 2019 09:32:52: start model_add_line... INFO @ Mon, 03 Jun 2019 09:32:52: start X-correlation... INFO @ Mon, 03 Jun 2019 09:32:52: end of X-cor INFO @ Mon, 03 Jun 2019 09:32:52: #2 finished! INFO @ Mon, 03 Jun 2019 09:32:52: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 09:32:52: #2 alternative fragment length(s) may be 2,203,232 bps INFO @ Mon, 03 Jun 2019 09:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.20_model.r INFO @ Mon, 03 Jun 2019 09:32:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:32:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:32:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:32:58: #1 total tags in treatment: 15787102 INFO @ Mon, 03 Jun 2019 09:32:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:32:58: #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 09:32:58: #1 tags after filtering in treatment: 15787102 INFO @ Mon, 03 Jun 2019 09:32:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:32:58: #1 finished! INFO @ Mon, 03 Jun 2019 09:32:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:32:59: 13000000 INFO @ Mon, 03 Jun 2019 09:33:00: #2 number of paired peaks: 1582 INFO @ Mon, 03 Jun 2019 09:33:00: start model_add_line... INFO @ Mon, 03 Jun 2019 09:33:00: start X-correlation... INFO @ Mon, 03 Jun 2019 09:33:00: end of X-cor INFO @ Mon, 03 Jun 2019 09:33:00: #2 finished! INFO @ Mon, 03 Jun 2019 09:33:00: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 09:33:00: #2 alternative fragment length(s) may be 2,203,232 bps INFO @ Mon, 03 Jun 2019 09:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.05_model.r INFO @ Mon, 03 Jun 2019 09:33:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:33:08: 14000000 INFO @ Mon, 03 Jun 2019 09:33:17: 15000000 INFO @ Mon, 03 Jun 2019 09:33:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:33:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:33:24: #1 total tags in treatment: 15787102 INFO @ Mon, 03 Jun 2019 09:33:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:33:24: #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 09:33:25: #1 tags after filtering in treatment: 15787102 INFO @ Mon, 03 Jun 2019 09:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:33:25: #1 finished! INFO @ Mon, 03 Jun 2019 09:33:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:33:26: #2 number of paired peaks: 1582 INFO @ Mon, 03 Jun 2019 09:33:26: start model_add_line... INFO @ Mon, 03 Jun 2019 09:33:27: start X-correlation... INFO @ Mon, 03 Jun 2019 09:33:27: end of X-cor INFO @ Mon, 03 Jun 2019 09:33:27: #2 finished! INFO @ Mon, 03 Jun 2019 09:33:27: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 09:33:27: #2 alternative fragment length(s) may be 2,203,232 bps INFO @ Mon, 03 Jun 2019 09:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.10_model.r INFO @ Mon, 03 Jun 2019 09:33:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:33:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:33:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.20_summits.bed INFO @ Mon, 03 Jun 2019 09:34:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.05_summits.bed INFO @ Mon, 03 Jun 2019 09:34:13: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4508 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:34:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:34:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287767/SRX287767.10_summits.bed INFO @ Mon, 03 Jun 2019 09:34:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2060 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。