Job ID = 1303616 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:25:50 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' 2019-06-03T11:25:50 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/sra72/SRR/007924/SRR8114851' 2019-06-03T11:25:50 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8114851' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T11:25:50 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T11:26:28 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 ) 2019-06-03T11:29:30 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 ) 2019-06-03T11:34:55 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 ) 2019-06-03T11:34:55 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 ) 2019-06-03T11:36:57 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 ) 2019-06-03T11:37:28 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 ) 2019-06-03T11:39:33 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 : 25,999,231 reads read : 51,998,462 reads written : 25,999,231 reads 0-length : 25,999,231 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: 00:11:38 25999231 reads; of these: 25999231 (100.00%) were unpaired; of these: 3174259 (12.21%) aligned 0 times 17417077 (66.99%) aligned exactly 1 time 5407895 (20.80%) aligned >1 times 87.79% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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] 7289897 / 22824972 = 0.3194 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 21:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.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 21:15:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:15:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.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 21:15:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:15:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.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 21:15:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:15:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:15:44: 1000000 INFO @ Mon, 03 Jun 2019 21:15:44: 1000000 INFO @ Mon, 03 Jun 2019 21:15:44: 1000000 INFO @ Mon, 03 Jun 2019 21:15:55: 2000000 INFO @ Mon, 03 Jun 2019 21:15:55: 2000000 INFO @ Mon, 03 Jun 2019 21:15:56: 2000000 INFO @ Mon, 03 Jun 2019 21:16:06: 3000000 INFO @ Mon, 03 Jun 2019 21:16:06: 3000000 INFO @ Mon, 03 Jun 2019 21:16:07: 3000000 INFO @ Mon, 03 Jun 2019 21:16:17: 4000000 INFO @ Mon, 03 Jun 2019 21:16:17: 4000000 INFO @ Mon, 03 Jun 2019 21:16:19: 4000000 INFO @ Mon, 03 Jun 2019 21:16:28: 5000000 INFO @ Mon, 03 Jun 2019 21:16:28: 5000000 INFO @ Mon, 03 Jun 2019 21:16:30: 5000000 INFO @ Mon, 03 Jun 2019 21:16:39: 6000000 INFO @ Mon, 03 Jun 2019 21:16:39: 6000000 INFO @ Mon, 03 Jun 2019 21:16:42: 6000000 INFO @ Mon, 03 Jun 2019 21:16:50: 7000000 INFO @ Mon, 03 Jun 2019 21:16:50: 7000000 INFO @ Mon, 03 Jun 2019 21:16:54: 7000000 INFO @ Mon, 03 Jun 2019 21:17:01: 8000000 INFO @ Mon, 03 Jun 2019 21:17:01: 8000000 INFO @ Mon, 03 Jun 2019 21:17:05: 8000000 INFO @ Mon, 03 Jun 2019 21:17:11: 9000000 INFO @ Mon, 03 Jun 2019 21:17:11: 9000000 INFO @ Mon, 03 Jun 2019 21:17:17: 9000000 INFO @ Mon, 03 Jun 2019 21:17:22: 10000000 INFO @ Mon, 03 Jun 2019 21:17:22: 10000000 INFO @ Mon, 03 Jun 2019 21:17:28: 10000000 INFO @ Mon, 03 Jun 2019 21:17:33: 11000000 INFO @ Mon, 03 Jun 2019 21:17:33: 11000000 INFO @ Mon, 03 Jun 2019 21:17:40: 11000000 INFO @ Mon, 03 Jun 2019 21:17:44: 12000000 INFO @ Mon, 03 Jun 2019 21:17:44: 12000000 INFO @ Mon, 03 Jun 2019 21:17:51: 12000000 INFO @ Mon, 03 Jun 2019 21:17:55: 13000000 INFO @ Mon, 03 Jun 2019 21:17:55: 13000000 INFO @ Mon, 03 Jun 2019 21:18:03: 13000000 INFO @ Mon, 03 Jun 2019 21:18:06: 14000000 INFO @ Mon, 03 Jun 2019 21:18:06: 14000000 INFO @ Mon, 03 Jun 2019 21:18:15: 14000000 INFO @ Mon, 03 Jun 2019 21:18:17: 15000000 INFO @ Mon, 03 Jun 2019 21:18:17: 15000000 INFO @ Mon, 03 Jun 2019 21:18:23: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 21:18:23: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 21:18:23: #1 total tags in treatment: 15535075 INFO @ Mon, 03 Jun 2019 21:18:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:18:23: #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 21:18:23: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 21:18:23: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 21:18:23: #1 total tags in treatment: 15535075 INFO @ Mon, 03 Jun 2019 21:18:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:18:23: #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 21:18:23: #1 tags after filtering in treatment: 15535075 INFO @ Mon, 03 Jun 2019 21:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:18:23: #1 finished! INFO @ Mon, 03 Jun 2019 21:18:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:18:23: #1 tags after filtering in treatment: 15535075 INFO @ Mon, 03 Jun 2019 21:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:18:23: #1 finished! INFO @ Mon, 03 Jun 2019 21:18:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:18:25: #2 number of paired peaks: 5632 INFO @ Mon, 03 Jun 2019 21:18:25: start model_add_line... INFO @ Mon, 03 Jun 2019 21:18:25: #2 number of paired peaks: 5632 INFO @ Mon, 03 Jun 2019 21:18:25: start model_add_line... INFO @ Mon, 03 Jun 2019 21:18:25: start X-correlation... INFO @ Mon, 03 Jun 2019 21:18:25: start X-correlation... INFO @ Mon, 03 Jun 2019 21:18:25: end of X-cor INFO @ Mon, 03 Jun 2019 21:18:25: end of X-cor INFO @ Mon, 03 Jun 2019 21:18:25: #2 finished! INFO @ Mon, 03 Jun 2019 21:18:25: #2 finished! INFO @ Mon, 03 Jun 2019 21:18:25: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 21:18:25: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 21:18:25: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 21:18:25: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 21:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.05_model.r INFO @ Mon, 03 Jun 2019 21:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.10_model.r INFO @ Mon, 03 Jun 2019 21:18:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:18:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:18:26: 15000000 INFO @ Mon, 03 Jun 2019 21:18:32: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 21:18:32: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 21:18:32: #1 total tags in treatment: 15535075 INFO @ Mon, 03 Jun 2019 21:18:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:18:32: #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 21:18:32: #1 tags after filtering in treatment: 15535075 INFO @ Mon, 03 Jun 2019 21:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:18:32: #1 finished! INFO @ Mon, 03 Jun 2019 21:18:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:18:35: #2 number of paired peaks: 5632 INFO @ Mon, 03 Jun 2019 21:18:35: start model_add_line... INFO @ Mon, 03 Jun 2019 21:18:35: start X-correlation... INFO @ Mon, 03 Jun 2019 21:18:35: end of X-cor INFO @ Mon, 03 Jun 2019 21:18:35: #2 finished! INFO @ Mon, 03 Jun 2019 21:18:35: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 21:18:35: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 21:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.20_model.r INFO @ Mon, 03 Jun 2019 21:18:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:19:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:19:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:19:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.10_summits.bed INFO @ Mon, 03 Jun 2019 21:19:49: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8994 records, 4 fields): 20 millis INFO @ Mon, 03 Jun 2019 21:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.05_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.05_summits.bed INFO @ Mon, 03 Jun 2019 21:19:50: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11125 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 21:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941148/SRX4941148.20_summits.bed INFO @ Mon, 03 Jun 2019 21:19:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6515 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。