Job ID = 1295122 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:00:39 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T03:00:39 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra20/SRR/000919/SRR942038' 2019-06-03T03:00:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR942038', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T03:03:51 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 ) 2019-06-03T03:03:51 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 ) 2019-06-03T03:03:51 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 ) 2019-06-03T03:03:51 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 : 22,343,535 reads read : 22,343,535 reads written : 22,343,535 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: 00:08:53 22343535 reads; of these: 22343535 (100.00%) were unpaired; of these: 1371166 (6.14%) aligned 0 times 13569457 (60.73%) aligned exactly 1 time 7402912 (33.13%) aligned >1 times 93.86% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 4694958 / 20972369 = 0.2239 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 12:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.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 12:27:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:27:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.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 12:27:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:27:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.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 12:27:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:27:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:27:28: 1000000 INFO @ Mon, 03 Jun 2019 12:27:28: 1000000 INFO @ Mon, 03 Jun 2019 12:27:29: 1000000 INFO @ Mon, 03 Jun 2019 12:27:38: 2000000 INFO @ Mon, 03 Jun 2019 12:27:38: 2000000 INFO @ Mon, 03 Jun 2019 12:27:38: 2000000 INFO @ Mon, 03 Jun 2019 12:27:46: 3000000 INFO @ Mon, 03 Jun 2019 12:27:47: 3000000 INFO @ Mon, 03 Jun 2019 12:27:47: 3000000 INFO @ Mon, 03 Jun 2019 12:27:55: 4000000 INFO @ Mon, 03 Jun 2019 12:27:55: 4000000 INFO @ Mon, 03 Jun 2019 12:27:55: 4000000 INFO @ Mon, 03 Jun 2019 12:28:04: 5000000 INFO @ Mon, 03 Jun 2019 12:28:04: 5000000 INFO @ Mon, 03 Jun 2019 12:28:04: 5000000 INFO @ Mon, 03 Jun 2019 12:28:11: 6000000 INFO @ Mon, 03 Jun 2019 12:28:14: 6000000 INFO @ Mon, 03 Jun 2019 12:28:14: 6000000 INFO @ Mon, 03 Jun 2019 12:28:19: 7000000 INFO @ Mon, 03 Jun 2019 12:28:25: 7000000 INFO @ Mon, 03 Jun 2019 12:28:25: 7000000 INFO @ Mon, 03 Jun 2019 12:28:27: 8000000 INFO @ Mon, 03 Jun 2019 12:28:35: 9000000 INFO @ Mon, 03 Jun 2019 12:28:35: 8000000 INFO @ Mon, 03 Jun 2019 12:28:35: 8000000 INFO @ Mon, 03 Jun 2019 12:28:43: 10000000 INFO @ Mon, 03 Jun 2019 12:28:44: 9000000 INFO @ Mon, 03 Jun 2019 12:28:44: 9000000 INFO @ Mon, 03 Jun 2019 12:28:50: 11000000 INFO @ Mon, 03 Jun 2019 12:28:54: 10000000 INFO @ Mon, 03 Jun 2019 12:28:54: 10000000 INFO @ Mon, 03 Jun 2019 12:28:59: 12000000 INFO @ Mon, 03 Jun 2019 12:29:04: 11000000 INFO @ Mon, 03 Jun 2019 12:29:04: 11000000 INFO @ Mon, 03 Jun 2019 12:29:07: 13000000 INFO @ Mon, 03 Jun 2019 12:29:13: 12000000 INFO @ Mon, 03 Jun 2019 12:29:13: 12000000 INFO @ Mon, 03 Jun 2019 12:29:15: 14000000 INFO @ Mon, 03 Jun 2019 12:29:22: 13000000 INFO @ Mon, 03 Jun 2019 12:29:22: 13000000 INFO @ Mon, 03 Jun 2019 12:29:23: 15000000 INFO @ Mon, 03 Jun 2019 12:29:30: 16000000 INFO @ Mon, 03 Jun 2019 12:29:32: 14000000 INFO @ Mon, 03 Jun 2019 12:29:32: 14000000 INFO @ Mon, 03 Jun 2019 12:29:33: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:29:33: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:29:33: #1 total tags in treatment: 16277411 INFO @ Mon, 03 Jun 2019 12:29:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:29:33: #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 12:29:33: #1 tags after filtering in treatment: 16277411 INFO @ Mon, 03 Jun 2019 12:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:29:33: #1 finished! INFO @ Mon, 03 Jun 2019 12:29:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:29:35: #2 number of paired peaks: 2125 INFO @ Mon, 03 Jun 2019 12:29:35: start model_add_line... INFO @ Mon, 03 Jun 2019 12:29:35: start X-correlation... INFO @ Mon, 03 Jun 2019 12:29:35: end of X-cor INFO @ Mon, 03 Jun 2019 12:29:35: #2 finished! INFO @ Mon, 03 Jun 2019 12:29:35: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 12:29:35: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 12:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.05_model.r INFO @ Mon, 03 Jun 2019 12:29:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:29:42: 15000000 INFO @ Mon, 03 Jun 2019 12:29:42: 15000000 INFO @ Mon, 03 Jun 2019 12:29:52: 16000000 INFO @ Mon, 03 Jun 2019 12:29:52: 16000000 INFO @ Mon, 03 Jun 2019 12:29:54: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:29:54: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:29:54: #1 total tags in treatment: 16277411 INFO @ Mon, 03 Jun 2019 12:29:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:29:54: #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 12:29:54: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:29:54: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:29:54: #1 total tags in treatment: 16277411 INFO @ Mon, 03 Jun 2019 12:29:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:29:54: #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 12:29:55: #1 tags after filtering in treatment: 16277411 INFO @ Mon, 03 Jun 2019 12:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:29:55: #1 finished! INFO @ Mon, 03 Jun 2019 12:29:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:29:55: #1 tags after filtering in treatment: 16277411 INFO @ Mon, 03 Jun 2019 12:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:29:55: #1 finished! INFO @ Mon, 03 Jun 2019 12:29:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:29:56: #2 number of paired peaks: 2125 INFO @ Mon, 03 Jun 2019 12:29:56: start model_add_line... INFO @ Mon, 03 Jun 2019 12:29:56: #2 number of paired peaks: 2125 INFO @ Mon, 03 Jun 2019 12:29:56: start model_add_line... INFO @ Mon, 03 Jun 2019 12:29:56: start X-correlation... INFO @ Mon, 03 Jun 2019 12:29:57: end of X-cor INFO @ Mon, 03 Jun 2019 12:29:57: #2 finished! INFO @ Mon, 03 Jun 2019 12:29:57: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 12:29:57: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 12:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.20_model.r INFO @ Mon, 03 Jun 2019 12:29:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:29:57: start X-correlation... INFO @ Mon, 03 Jun 2019 12:29:57: end of X-cor INFO @ Mon, 03 Jun 2019 12:29:57: #2 finished! INFO @ Mon, 03 Jun 2019 12:29:57: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 12:29:57: #2 alternative fragment length(s) may be 198 bps INFO @ Mon, 03 Jun 2019 12:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.10_model.r INFO @ Mon, 03 Jun 2019 12:29:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:30:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:30:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:30:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.05_summits.bed INFO @ Mon, 03 Jun 2019 12:30:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9792 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.20_summits.bed INFO @ Mon, 03 Jun 2019 12:31:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5423 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326965/SRX326965.10_summits.bed INFO @ Mon, 03 Jun 2019 12:31:13: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7631 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。