Job ID = 1294354 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:38:49 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T21:38:49 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.18' 2019-06-02T21:38:49 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '172.19.7.18' 2019-06-02T21:38:49 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra46/SRR/005188/SRR5312694' 2019-06-02T21:38:58 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR5312694' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T21:38:58 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T21:42:11 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 ) 2019-06-02T21:42:11 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 ) 2019-06-02T21:46:45 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 ) 2019-06-02T21:46:45 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 ) 2019-06-02T21:46:45 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 : 31,008,215 reads read : 62,016,430 reads written : 62,016,430 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: 00:58:11 31008215 reads; of these: 31008215 (100.00%) were paired; of these: 5389239 (17.38%) aligned concordantly 0 times 20376384 (65.71%) aligned concordantly exactly 1 time 5242592 (16.91%) aligned concordantly >1 times ---- 5389239 pairs aligned concordantly 0 times; of these: 320474 (5.95%) aligned discordantly 1 time ---- 5068765 pairs aligned 0 times concordantly or discordantly; of these: 10137530 mates make up the pairs; of these: 9071096 (89.48%) aligned 0 times 604584 (5.96%) aligned exactly 1 time 461850 (4.56%) aligned >1 times 85.37% overall alignment rate Time searching: 00:58:11 Overall time: 00:58:11 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 24 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] 7503916 / 25918649 = 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 08:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.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 08:55:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.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 08:55:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.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 08:55:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:36: 1000000 INFO @ Mon, 03 Jun 2019 08:55:36: 1000000 INFO @ Mon, 03 Jun 2019 08:55:37: 1000000 INFO @ Mon, 03 Jun 2019 08:55:43: 2000000 INFO @ Mon, 03 Jun 2019 08:55:43: 2000000 INFO @ Mon, 03 Jun 2019 08:55:44: 2000000 INFO @ Mon, 03 Jun 2019 08:55:50: 3000000 INFO @ Mon, 03 Jun 2019 08:55:50: 3000000 INFO @ Mon, 03 Jun 2019 08:55:52: 3000000 INFO @ Mon, 03 Jun 2019 08:55:58: 4000000 INFO @ Mon, 03 Jun 2019 08:55:58: 4000000 INFO @ Mon, 03 Jun 2019 08:55:59: 4000000 INFO @ Mon, 03 Jun 2019 08:56:05: 5000000 INFO @ Mon, 03 Jun 2019 08:56:05: 5000000 INFO @ Mon, 03 Jun 2019 08:56:07: 5000000 INFO @ Mon, 03 Jun 2019 08:56:12: 6000000 INFO @ Mon, 03 Jun 2019 08:56:12: 6000000 INFO @ Mon, 03 Jun 2019 08:56:14: 6000000 INFO @ Mon, 03 Jun 2019 08:56:19: 7000000 INFO @ Mon, 03 Jun 2019 08:56:19: 7000000 INFO @ Mon, 03 Jun 2019 08:56:22: 7000000 INFO @ Mon, 03 Jun 2019 08:56:26: 8000000 INFO @ Mon, 03 Jun 2019 08:56:26: 8000000 INFO @ Mon, 03 Jun 2019 08:56:29: 8000000 INFO @ Mon, 03 Jun 2019 08:56:33: 9000000 INFO @ Mon, 03 Jun 2019 08:56:33: 9000000 INFO @ Mon, 03 Jun 2019 08:56:37: 9000000 INFO @ Mon, 03 Jun 2019 08:56:40: 10000000 INFO @ Mon, 03 Jun 2019 08:56:40: 10000000 INFO @ Mon, 03 Jun 2019 08:56:45: 10000000 INFO @ Mon, 03 Jun 2019 08:56:47: 11000000 INFO @ Mon, 03 Jun 2019 08:56:47: 11000000 INFO @ Mon, 03 Jun 2019 08:56:51: 11000000 INFO @ Mon, 03 Jun 2019 08:56:54: 12000000 INFO @ Mon, 03 Jun 2019 08:56:54: 12000000 INFO @ Mon, 03 Jun 2019 08:56:59: 12000000 INFO @ Mon, 03 Jun 2019 08:57:01: 13000000 INFO @ Mon, 03 Jun 2019 08:57:01: 13000000 INFO @ Mon, 03 Jun 2019 08:57:05: 13000000 INFO @ Mon, 03 Jun 2019 08:57:08: 14000000 INFO @ Mon, 03 Jun 2019 08:57:08: 14000000 INFO @ Mon, 03 Jun 2019 08:57:12: 14000000 INFO @ Mon, 03 Jun 2019 08:57:15: 15000000 INFO @ Mon, 03 Jun 2019 08:57:15: 15000000 INFO @ Mon, 03 Jun 2019 08:57:19: 15000000 INFO @ Mon, 03 Jun 2019 08:57:21: 16000000 INFO @ Mon, 03 Jun 2019 08:57:22: 16000000 INFO @ Mon, 03 Jun 2019 08:57:26: 16000000 INFO @ Mon, 03 Jun 2019 08:57:28: 17000000 INFO @ Mon, 03 Jun 2019 08:57:29: 17000000 INFO @ Mon, 03 Jun 2019 08:57:33: 17000000 INFO @ Mon, 03 Jun 2019 08:57:35: 18000000 INFO @ Mon, 03 Jun 2019 08:57:36: 18000000 INFO @ Mon, 03 Jun 2019 08:57:40: 18000000 INFO @ Mon, 03 Jun 2019 08:57:42: 19000000 INFO @ Mon, 03 Jun 2019 08:57:43: 19000000 INFO @ Mon, 03 Jun 2019 08:57:47: 19000000 INFO @ Mon, 03 Jun 2019 08:57:49: 20000000 INFO @ Mon, 03 Jun 2019 08:57:50: 20000000 INFO @ Mon, 03 Jun 2019 08:57:54: 20000000 INFO @ Mon, 03 Jun 2019 08:57:56: 21000000 INFO @ Mon, 03 Jun 2019 08:57:57: 21000000 INFO @ Mon, 03 Jun 2019 08:58:00: 21000000 INFO @ Mon, 03 Jun 2019 08:58:02: 22000000 INFO @ Mon, 03 Jun 2019 08:58:04: 22000000 INFO @ Mon, 03 Jun 2019 08:58:07: 22000000 INFO @ Mon, 03 Jun 2019 08:58:09: 23000000 INFO @ Mon, 03 Jun 2019 08:58:11: 23000000 INFO @ Mon, 03 Jun 2019 08:58:14: 23000000 INFO @ Mon, 03 Jun 2019 08:58:16: 24000000 INFO @ Mon, 03 Jun 2019 08:58:17: 24000000 INFO @ Mon, 03 Jun 2019 08:58:20: 24000000 INFO @ Mon, 03 Jun 2019 08:58:22: 25000000 INFO @ Mon, 03 Jun 2019 08:58:24: 25000000 INFO @ Mon, 03 Jun 2019 08:58:27: 25000000 INFO @ Mon, 03 Jun 2019 08:58:29: 26000000 INFO @ Mon, 03 Jun 2019 08:58:31: 26000000 INFO @ Mon, 03 Jun 2019 08:58:34: 26000000 INFO @ Mon, 03 Jun 2019 08:58:36: 27000000 INFO @ Mon, 03 Jun 2019 08:58:38: 27000000 INFO @ Mon, 03 Jun 2019 08:58:40: 27000000 INFO @ Mon, 03 Jun 2019 08:58:43: 28000000 INFO @ Mon, 03 Jun 2019 08:58:45: 28000000 INFO @ Mon, 03 Jun 2019 08:58:47: 28000000 INFO @ Mon, 03 Jun 2019 08:58:49: 29000000 INFO @ Mon, 03 Jun 2019 08:58:52: 29000000 INFO @ Mon, 03 Jun 2019 08:58:53: 29000000 INFO @ Mon, 03 Jun 2019 08:58:57: 30000000 INFO @ Mon, 03 Jun 2019 08:58:59: 30000000 INFO @ Mon, 03 Jun 2019 08:59:00: 30000000 INFO @ Mon, 03 Jun 2019 08:59:03: 31000000 INFO @ Mon, 03 Jun 2019 08:59:05: 31000000 INFO @ Mon, 03 Jun 2019 08:59:07: 31000000 INFO @ Mon, 03 Jun 2019 08:59:10: 32000000 INFO @ Mon, 03 Jun 2019 08:59:12: 32000000 INFO @ Mon, 03 Jun 2019 08:59:13: 32000000 INFO @ Mon, 03 Jun 2019 08:59:17: 33000000 INFO @ Mon, 03 Jun 2019 08:59:19: 33000000 INFO @ Mon, 03 Jun 2019 08:59:20: 33000000 INFO @ Mon, 03 Jun 2019 08:59:23: 34000000 INFO @ Mon, 03 Jun 2019 08:59:25: 34000000 INFO @ Mon, 03 Jun 2019 08:59:27: 34000000 INFO @ Mon, 03 Jun 2019 08:59:30: 35000000 INFO @ Mon, 03 Jun 2019 08:59:32: 35000000 INFO @ Mon, 03 Jun 2019 08:59:33: 35000000 INFO @ Mon, 03 Jun 2019 08:59:36: 36000000 INFO @ Mon, 03 Jun 2019 08:59:39: 36000000 INFO @ Mon, 03 Jun 2019 08:59:40: 36000000 INFO @ Mon, 03 Jun 2019 08:59:43: 37000000 INFO @ Mon, 03 Jun 2019 08:59:45: 37000000 INFO @ Mon, 03 Jun 2019 08:59:46: 37000000 INFO @ Mon, 03 Jun 2019 08:59:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:59:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:59:50: #1 total tags in treatment: 18146995 INFO @ Mon, 03 Jun 2019 08:59:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:59:50: #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 08:59:50: #1 tags after filtering in treatment: 15205798 INFO @ Mon, 03 Jun 2019 08:59:50: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 03 Jun 2019 08:59:50: #1 finished! INFO @ Mon, 03 Jun 2019 08:59:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:59:52: #2 number of paired peaks: 3292 INFO @ Mon, 03 Jun 2019 08:59:52: start model_add_line... INFO @ Mon, 03 Jun 2019 08:59:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:59:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:59:52: #1 total tags in treatment: 18146995 INFO @ Mon, 03 Jun 2019 08:59:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:59:52: #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 08:59:52: start X-correlation... INFO @ Mon, 03 Jun 2019 08:59:52: end of X-cor INFO @ Mon, 03 Jun 2019 08:59:52: #2 finished! INFO @ Mon, 03 Jun 2019 08:59:52: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 08:59:52: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 08:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.20_model.r INFO @ Mon, 03 Jun 2019 08:59:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:59:52: #1 tags after filtering in treatment: 15205798 INFO @ Mon, 03 Jun 2019 08:59:52: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 03 Jun 2019 08:59:52: #1 finished! INFO @ Mon, 03 Jun 2019 08:59:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:59:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:59:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:59:53: #1 total tags in treatment: 18146995 INFO @ Mon, 03 Jun 2019 08:59:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:59:53: #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 08:59:53: #1 tags after filtering in treatment: 15205798 INFO @ Mon, 03 Jun 2019 08:59:53: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 03 Jun 2019 08:59:53: #1 finished! INFO @ Mon, 03 Jun 2019 08:59:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:59:54: #2 number of paired peaks: 3292 INFO @ Mon, 03 Jun 2019 08:59:54: start model_add_line... INFO @ Mon, 03 Jun 2019 08:59:54: start X-correlation... INFO @ Mon, 03 Jun 2019 08:59:54: end of X-cor INFO @ Mon, 03 Jun 2019 08:59:54: #2 finished! INFO @ Mon, 03 Jun 2019 08:59:54: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 08:59:54: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 08:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.10_model.r INFO @ Mon, 03 Jun 2019 08:59:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:59:55: #2 number of paired peaks: 3292 INFO @ Mon, 03 Jun 2019 08:59:55: start model_add_line... INFO @ Mon, 03 Jun 2019 08:59:55: start X-correlation... INFO @ Mon, 03 Jun 2019 08:59:55: end of X-cor INFO @ Mon, 03 Jun 2019 08:59:55: #2 finished! INFO @ Mon, 03 Jun 2019 08:59:55: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 08:59:55: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 08:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.05_model.r INFO @ Mon, 03 Jun 2019 08:59:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:00:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:00:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:00:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:01:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:01:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:01:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.20_summits.bed INFO @ Mon, 03 Jun 2019 09:01:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4561 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:01:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:01:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:01:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.10_summits.bed INFO @ Mon, 03 Jun 2019 09:01:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6558 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:01:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:01:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612519/SRX2612519.05_summits.bed INFO @ Mon, 03 Jun 2019 09:01:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8314 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。