Job ID = 1295146 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:10:28 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' 2019-06-03T03:10:28 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/sra53/SRR/006024/SRR6168912' 2019-06-03T03:10:28 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR6168912' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T03:10:28 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T03:20:41 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 ) 2019-06-03T03:20:41 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 ) 2019-06-03T03:20:41 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 ) 2019-06-03T03:23:48 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 : 37,954,503 reads read : 75,909,006 reads written : 37,954,503 reads 0-length : 37,954,503 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: 00:07:53 37954503 reads; of these: 37954503 (100.00%) were unpaired; of these: 5642497 (14.87%) aligned 0 times 30610637 (80.65%) aligned exactly 1 time 1701369 (4.48%) aligned >1 times 85.13% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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 16 files... [bam_rmdupse_core] 14415157 / 32312006 = 0.4461 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 13:00:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.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 13:00:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.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 13:00:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.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 13:00:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:48: 1000000 INFO @ Mon, 03 Jun 2019 13:00:49: 1000000 INFO @ Mon, 03 Jun 2019 13:00:49: 1000000 INFO @ Mon, 03 Jun 2019 13:00:57: 2000000 INFO @ Mon, 03 Jun 2019 13:00:59: 2000000 INFO @ Mon, 03 Jun 2019 13:00:59: 2000000 INFO @ Mon, 03 Jun 2019 13:01:05: 3000000 INFO @ Mon, 03 Jun 2019 13:01:08: 3000000 INFO @ Mon, 03 Jun 2019 13:01:10: 3000000 INFO @ Mon, 03 Jun 2019 13:01:14: 4000000 INFO @ Mon, 03 Jun 2019 13:01:18: 4000000 INFO @ Mon, 03 Jun 2019 13:01:21: 4000000 INFO @ Mon, 03 Jun 2019 13:01:22: 5000000 INFO @ Mon, 03 Jun 2019 13:01:28: 5000000 INFO @ Mon, 03 Jun 2019 13:01:30: 6000000 INFO @ Mon, 03 Jun 2019 13:01:32: 5000000 INFO @ Mon, 03 Jun 2019 13:01:37: 6000000 INFO @ Mon, 03 Jun 2019 13:01:39: 7000000 INFO @ Mon, 03 Jun 2019 13:01:42: 6000000 INFO @ Mon, 03 Jun 2019 13:01:47: 7000000 INFO @ Mon, 03 Jun 2019 13:01:48: 8000000 INFO @ Mon, 03 Jun 2019 13:01:52: 7000000 INFO @ Mon, 03 Jun 2019 13:01:56: 8000000 INFO @ Mon, 03 Jun 2019 13:01:57: 9000000 INFO @ Mon, 03 Jun 2019 13:02:02: 8000000 INFO @ Mon, 03 Jun 2019 13:02:05: 10000000 INFO @ Mon, 03 Jun 2019 13:02:06: 9000000 INFO @ Mon, 03 Jun 2019 13:02:12: 9000000 INFO @ Mon, 03 Jun 2019 13:02:13: 11000000 INFO @ Mon, 03 Jun 2019 13:02:15: 10000000 INFO @ Mon, 03 Jun 2019 13:02:22: 12000000 INFO @ Mon, 03 Jun 2019 13:02:22: 10000000 INFO @ Mon, 03 Jun 2019 13:02:24: 11000000 INFO @ Mon, 03 Jun 2019 13:02:30: 13000000 INFO @ Mon, 03 Jun 2019 13:02:32: 11000000 INFO @ Mon, 03 Jun 2019 13:02:34: 12000000 INFO @ Mon, 03 Jun 2019 13:02:40: 14000000 INFO @ Mon, 03 Jun 2019 13:02:42: 12000000 INFO @ Mon, 03 Jun 2019 13:02:44: 13000000 INFO @ Mon, 03 Jun 2019 13:02:50: 15000000 INFO @ Mon, 03 Jun 2019 13:02:52: 13000000 INFO @ Mon, 03 Jun 2019 13:02:53: 14000000 INFO @ Mon, 03 Jun 2019 13:02:59: 16000000 INFO @ Mon, 03 Jun 2019 13:03:02: 14000000 INFO @ Mon, 03 Jun 2019 13:03:04: 15000000 INFO @ Mon, 03 Jun 2019 13:03:09: 17000000 INFO @ Mon, 03 Jun 2019 13:03:14: 16000000 INFO @ Mon, 03 Jun 2019 13:03:14: 15000000 INFO @ Mon, 03 Jun 2019 13:03:18: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 13:03:18: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 13:03:18: #1 total tags in treatment: 17896849 INFO @ Mon, 03 Jun 2019 13:03:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:18: #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 13:03:18: #1 tags after filtering in treatment: 17896849 INFO @ Mon, 03 Jun 2019 13:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:18: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:22: #2 number of paired peaks: 15949 INFO @ Mon, 03 Jun 2019 13:03:22: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:22: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:22: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:22: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:22: #2 predicted fragment length is 157 bps INFO @ Mon, 03 Jun 2019 13:03:22: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 03 Jun 2019 13:03:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.05_model.r INFO @ Mon, 03 Jun 2019 13:03:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:03:24: 17000000 INFO @ Mon, 03 Jun 2019 13:03:26: 16000000 INFO @ Mon, 03 Jun 2019 13:03:32: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 13:03:32: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 13:03:32: #1 total tags in treatment: 17896849 INFO @ Mon, 03 Jun 2019 13:03:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:32: #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 13:03:33: #1 tags after filtering in treatment: 17896849 INFO @ Mon, 03 Jun 2019 13:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:33: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:36: #2 number of paired peaks: 15949 INFO @ Mon, 03 Jun 2019 13:03:36: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:37: 17000000 INFO @ Mon, 03 Jun 2019 13:03:37: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:37: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:37: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:37: #2 predicted fragment length is 157 bps INFO @ Mon, 03 Jun 2019 13:03:37: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 03 Jun 2019 13:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.10_model.r INFO @ Mon, 03 Jun 2019 13:03:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:03:47: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 13:03:47: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 13:03:47: #1 total tags in treatment: 17896849 INFO @ Mon, 03 Jun 2019 13:03:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:47: #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 13:03:47: #1 tags after filtering in treatment: 17896849 INFO @ Mon, 03 Jun 2019 13:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:47: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:50: #2 number of paired peaks: 15949 INFO @ Mon, 03 Jun 2019 13:03:50: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:51: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:51: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:51: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:51: #2 predicted fragment length is 157 bps INFO @ Mon, 03 Jun 2019 13:03:51: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 03 Jun 2019 13:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.20_model.r INFO @ Mon, 03 Jun 2019 13:03:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 13:04:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.05_summits.bed INFO @ Mon, 03 Jun 2019 13:04:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8925 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 13:04:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.10_summits.bed INFO @ Mon, 03 Jun 2019 13:04:55: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8552 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279762/SRX3279762.20_summits.bed INFO @ Mon, 03 Jun 2019 13:05:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7925 records, 4 fields): 12 millis CompletedMACS2peakCalling