Job ID = 1294336 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:27:03 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' 2019-06-02T21:27:03 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/sra9/SRR/000768/SRR786746' 2019-06-02T21:27:12 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR786746' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T21:27:12 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T21:29:53 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 ) 2019-06-02T21:29:53 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 ) 2019-06-02T21:47:27 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 : 20,077,304 reads read : 40,154,608 reads written : 40,154,608 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: 00:26:30 20077304 reads; of these: 20077304 (100.00%) were paired; of these: 8821091 (43.94%) aligned concordantly 0 times 8796575 (43.81%) aligned concordantly exactly 1 time 2459638 (12.25%) aligned concordantly >1 times ---- 8821091 pairs aligned concordantly 0 times; of these: 8498 (0.10%) aligned discordantly 1 time ---- 8812593 pairs aligned 0 times concordantly or discordantly; of these: 17625186 mates make up the pairs; of these: 17394029 (98.69%) aligned 0 times 181722 (1.03%) aligned exactly 1 time 49435 (0.28%) aligned >1 times 56.68% overall alignment rate Time searching: 00:26:30 Overall time: 00:26:30 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3259100 / 11256115 = 0.2895 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 07:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.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 07:41:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:41:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.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 07:41:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:41:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.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 07:41:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:41:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:42:06: 1000000 INFO @ Mon, 03 Jun 2019 07:42:06: 1000000 INFO @ Mon, 03 Jun 2019 07:42:08: 1000000 INFO @ Mon, 03 Jun 2019 07:42:14: 2000000 INFO @ Mon, 03 Jun 2019 07:42:15: 2000000 INFO @ Mon, 03 Jun 2019 07:42:18: 2000000 INFO @ Mon, 03 Jun 2019 07:42:22: 3000000 INFO @ Mon, 03 Jun 2019 07:42:23: 3000000 INFO @ Mon, 03 Jun 2019 07:42:28: 3000000 INFO @ Mon, 03 Jun 2019 07:42:30: 4000000 INFO @ Mon, 03 Jun 2019 07:42:31: 4000000 INFO @ Mon, 03 Jun 2019 07:42:38: 4000000 INFO @ Mon, 03 Jun 2019 07:42:38: 5000000 INFO @ Mon, 03 Jun 2019 07:42:39: 5000000 INFO @ Mon, 03 Jun 2019 07:42:46: 6000000 INFO @ Mon, 03 Jun 2019 07:42:47: 5000000 INFO @ Mon, 03 Jun 2019 07:42:47: 6000000 INFO @ Mon, 03 Jun 2019 07:42:54: 7000000 INFO @ Mon, 03 Jun 2019 07:42:55: 7000000 INFO @ Mon, 03 Jun 2019 07:42:56: 6000000 INFO @ Mon, 03 Jun 2019 07:43:02: 8000000 INFO @ Mon, 03 Jun 2019 07:43:03: 8000000 INFO @ Mon, 03 Jun 2019 07:43:06: 7000000 INFO @ Mon, 03 Jun 2019 07:43:09: 9000000 INFO @ Mon, 03 Jun 2019 07:43:11: 9000000 INFO @ Mon, 03 Jun 2019 07:43:15: 8000000 INFO @ Mon, 03 Jun 2019 07:43:17: 10000000 INFO @ Mon, 03 Jun 2019 07:43:19: 10000000 INFO @ Mon, 03 Jun 2019 07:43:24: 9000000 INFO @ Mon, 03 Jun 2019 07:43:25: 11000000 INFO @ Mon, 03 Jun 2019 07:43:27: 11000000 INFO @ Mon, 03 Jun 2019 07:43:32: 12000000 INFO @ Mon, 03 Jun 2019 07:43:33: 10000000 INFO @ Mon, 03 Jun 2019 07:43:35: 12000000 INFO @ Mon, 03 Jun 2019 07:43:40: 13000000 INFO @ Mon, 03 Jun 2019 07:43:42: 11000000 INFO @ Mon, 03 Jun 2019 07:43:42: 13000000 INFO @ Mon, 03 Jun 2019 07:43:48: 14000000 INFO @ Mon, 03 Jun 2019 07:43:50: 14000000 INFO @ Mon, 03 Jun 2019 07:43:51: 12000000 INFO @ Mon, 03 Jun 2019 07:43:55: 15000000 INFO @ Mon, 03 Jun 2019 07:43:58: 15000000 INFO @ Mon, 03 Jun 2019 07:44:00: 13000000 INFO @ Mon, 03 Jun 2019 07:44:03: 16000000 INFO @ Mon, 03 Jun 2019 07:44:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:44:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:44:04: #1 total tags in treatment: 7998154 INFO @ Mon, 03 Jun 2019 07:44:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:44:04: #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 07:44:05: #1 tags after filtering in treatment: 6652047 INFO @ Mon, 03 Jun 2019 07:44:05: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 07:44:05: #1 finished! INFO @ Mon, 03 Jun 2019 07:44:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:44:05: 16000000 INFO @ Mon, 03 Jun 2019 07:44:05: #2 number of paired peaks: 1633 INFO @ Mon, 03 Jun 2019 07:44:05: start model_add_line... INFO @ Mon, 03 Jun 2019 07:44:05: start X-correlation... INFO @ Mon, 03 Jun 2019 07:44:06: end of X-cor INFO @ Mon, 03 Jun 2019 07:44:06: #2 finished! INFO @ Mon, 03 Jun 2019 07:44:06: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 07:44:06: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 07:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.10_model.r INFO @ Mon, 03 Jun 2019 07:44:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:44:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:44:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:44:07: #1 total tags in treatment: 7998154 INFO @ Mon, 03 Jun 2019 07:44:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:44:07: #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 07:44:07: #1 tags after filtering in treatment: 6652047 INFO @ Mon, 03 Jun 2019 07:44:07: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 07:44:07: #1 finished! INFO @ Mon, 03 Jun 2019 07:44:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:44:08: #2 number of paired peaks: 1633 INFO @ Mon, 03 Jun 2019 07:44:08: start model_add_line... INFO @ Mon, 03 Jun 2019 07:44:08: start X-correlation... INFO @ Mon, 03 Jun 2019 07:44:08: end of X-cor INFO @ Mon, 03 Jun 2019 07:44:08: #2 finished! INFO @ Mon, 03 Jun 2019 07:44:08: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 07:44:08: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 07:44:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.05_model.r INFO @ Mon, 03 Jun 2019 07:44:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:44:09: 14000000 INFO @ Mon, 03 Jun 2019 07:44:17: 15000000 INFO @ Mon, 03 Jun 2019 07:44:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:44:26: 16000000 INFO @ Mon, 03 Jun 2019 07:44:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:44:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:44:28: #1 total tags in treatment: 7998154 INFO @ Mon, 03 Jun 2019 07:44:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:44:28: #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 07:44:28: #1 tags after filtering in treatment: 6652047 INFO @ Mon, 03 Jun 2019 07:44:28: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 07:44:28: #1 finished! INFO @ Mon, 03 Jun 2019 07:44:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:44:29: #2 number of paired peaks: 1633 INFO @ Mon, 03 Jun 2019 07:44:29: start model_add_line... INFO @ Mon, 03 Jun 2019 07:44:29: start X-correlation... INFO @ Mon, 03 Jun 2019 07:44:29: end of X-cor INFO @ Mon, 03 Jun 2019 07:44:29: #2 finished! INFO @ Mon, 03 Jun 2019 07:44:29: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 07:44:29: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 07:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.20_model.r INFO @ Mon, 03 Jun 2019 07:44:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:44:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:44:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.10_summits.bed INFO @ Mon, 03 Jun 2019 07:44:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3850 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.05_summits.bed INFO @ Mon, 03 Jun 2019 07:44:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6644 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:44:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252226/SRX252226.20_summits.bed INFO @ Mon, 03 Jun 2019 07:44:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2258 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。