Job ID = 1295723 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:10:30 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' 2019-06-03T06:10:30 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/sra68/SRR/007408/SRR7586077' 2019-06-03T06:10:30 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR7586077' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T06:10:30 fasterq-dump.2.9.6 err: invalid accession 'SRR7586077' 2019-06-03T06:13:33 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 ) 2019-06-03T06:13:33 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 ) 2019-06-03T06:13:33 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 ) 2019-06-03T06:13:33 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 : 23,504,556 reads read : 47,009,112 reads written : 23,504,556 reads 0-length : 23,504,556 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: 00:12:34 23504556 reads; of these: 23504556 (100.00%) were unpaired; of these: 4009666 (17.06%) aligned 0 times 16677303 (70.95%) aligned exactly 1 time 2817587 (11.99%) aligned >1 times 82.94% overall alignment rate Time searching: 00:12:34 Overall time: 00:12:34 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] 5907780 / 19494890 = 0.3030 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 15:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.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 15:44:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:44:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.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 15:44:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:44:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.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 15:44:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:44:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:44:27: 1000000 INFO @ Mon, 03 Jun 2019 15:44:28: 1000000 INFO @ Mon, 03 Jun 2019 15:44:28: 1000000 INFO @ Mon, 03 Jun 2019 15:44:40: 2000000 INFO @ Mon, 03 Jun 2019 15:44:43: 2000000 INFO @ Mon, 03 Jun 2019 15:44:43: 2000000 INFO @ Mon, 03 Jun 2019 15:44:53: 3000000 INFO @ Mon, 03 Jun 2019 15:44:58: 3000000 INFO @ Mon, 03 Jun 2019 15:44:58: 3000000 INFO @ Mon, 03 Jun 2019 15:45:06: 4000000 INFO @ Mon, 03 Jun 2019 15:45:12: 4000000 INFO @ Mon, 03 Jun 2019 15:45:12: 4000000 INFO @ Mon, 03 Jun 2019 15:45:20: 5000000 INFO @ Mon, 03 Jun 2019 15:45:26: 5000000 INFO @ Mon, 03 Jun 2019 15:45:27: 5000000 INFO @ Mon, 03 Jun 2019 15:45:33: 6000000 INFO @ Mon, 03 Jun 2019 15:45:40: 6000000 INFO @ Mon, 03 Jun 2019 15:45:41: 6000000 INFO @ Mon, 03 Jun 2019 15:45:45: 7000000 INFO @ Mon, 03 Jun 2019 15:45:54: 7000000 INFO @ Mon, 03 Jun 2019 15:45:56: 7000000 INFO @ Mon, 03 Jun 2019 15:45:59: 8000000 INFO @ Mon, 03 Jun 2019 15:46:09: 8000000 INFO @ Mon, 03 Jun 2019 15:46:10: 8000000 INFO @ Mon, 03 Jun 2019 15:46:12: 9000000 INFO @ Mon, 03 Jun 2019 15:46:22: 9000000 INFO @ Mon, 03 Jun 2019 15:46:24: 9000000 INFO @ Mon, 03 Jun 2019 15:46:25: 10000000 INFO @ Mon, 03 Jun 2019 15:46:35: 10000000 INFO @ Mon, 03 Jun 2019 15:46:38: 11000000 INFO @ Mon, 03 Jun 2019 15:46:38: 10000000 INFO @ Mon, 03 Jun 2019 15:46:48: 11000000 INFO @ Mon, 03 Jun 2019 15:46:50: 12000000 INFO @ Mon, 03 Jun 2019 15:46:53: 11000000 INFO @ Mon, 03 Jun 2019 15:47:01: 12000000 INFO @ Mon, 03 Jun 2019 15:47:03: 13000000 INFO @ Mon, 03 Jun 2019 15:47:07: 12000000 INFO @ Mon, 03 Jun 2019 15:47:10: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 15:47:10: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 15:47:10: #1 total tags in treatment: 13587110 INFO @ Mon, 03 Jun 2019 15:47:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:47:10: #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 15:47:10: #1 tags after filtering in treatment: 13587110 INFO @ Mon, 03 Jun 2019 15:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:47:10: #1 finished! INFO @ Mon, 03 Jun 2019 15:47:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:47:12: #2 number of paired peaks: 1355 INFO @ Mon, 03 Jun 2019 15:47:12: start model_add_line... INFO @ Mon, 03 Jun 2019 15:47:12: start X-correlation... INFO @ Mon, 03 Jun 2019 15:47:12: end of X-cor INFO @ Mon, 03 Jun 2019 15:47:12: #2 finished! INFO @ Mon, 03 Jun 2019 15:47:12: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 15:47:12: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 15:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.20_model.r INFO @ Mon, 03 Jun 2019 15:47:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:47:15: 13000000 INFO @ Mon, 03 Jun 2019 15:47:21: 13000000 INFO @ Mon, 03 Jun 2019 15:47:22: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 15:47:22: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 15:47:22: #1 total tags in treatment: 13587110 INFO @ Mon, 03 Jun 2019 15:47:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:47:22: #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 15:47:23: #1 tags after filtering in treatment: 13587110 INFO @ Mon, 03 Jun 2019 15:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:47:23: #1 finished! INFO @ Mon, 03 Jun 2019 15:47:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:47:24: #2 number of paired peaks: 1355 INFO @ Mon, 03 Jun 2019 15:47:24: start model_add_line... INFO @ Mon, 03 Jun 2019 15:47:25: start X-correlation... INFO @ Mon, 03 Jun 2019 15:47:25: end of X-cor INFO @ Mon, 03 Jun 2019 15:47:25: #2 finished! INFO @ Mon, 03 Jun 2019 15:47:25: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 15:47:25: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 15:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.10_model.r INFO @ Mon, 03 Jun 2019 15:47:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:47:29: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 15:47:29: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 15:47:29: #1 total tags in treatment: 13587110 INFO @ Mon, 03 Jun 2019 15:47:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:47:29: #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 15:47:29: #1 tags after filtering in treatment: 13587110 INFO @ Mon, 03 Jun 2019 15:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:47:29: #1 finished! INFO @ Mon, 03 Jun 2019 15:47:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:47:31: #2 number of paired peaks: 1355 INFO @ Mon, 03 Jun 2019 15:47:31: start model_add_line... INFO @ Mon, 03 Jun 2019 15:47:31: start X-correlation... INFO @ Mon, 03 Jun 2019 15:47:31: end of X-cor INFO @ Mon, 03 Jun 2019 15:47:31: #2 finished! INFO @ Mon, 03 Jun 2019 15:47:31: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 15:47:31: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 15:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.05_model.r INFO @ Mon, 03 Jun 2019 15:47:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:48:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:48:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:48:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.20_summits.bed INFO @ Mon, 03 Jun 2019 15:48:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3396 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.10_summits.bed INFO @ Mon, 03 Jun 2019 15:48:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4650 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:48:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:48:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:48:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4451933/SRX4451933.05_summits.bed INFO @ Mon, 03 Jun 2019 15:48:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5763 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。