Job ID = 1293859 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:47:53 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 ) 2019-06-02T17:47:53 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.54' 2019-06-02T17:47:53 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' (130.14.250.25) from '172.19.7.54' 2019-06-02T17:47:53 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/sos/sra-pub-run-1/SRR2546857/SRR2546857.1' 2019-06-02T17:47:53 fasterq-dump.2.9.6 err: invalid accession 'SRR2546857' spots read : 10,674,202 reads read : 10,674,202 reads written : 10,674,202 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: 00:04:00 10674202 reads; of these: 10674202 (100.00%) were unpaired; of these: 633562 (5.94%) aligned 0 times 7956775 (74.54%) aligned exactly 1 time 2083865 (19.52%) aligned >1 times 94.06% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 1764513 / 10040640 = 0.1757 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 02:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.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 02:57:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:57:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.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 02:57:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:57:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.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 02:57:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:57:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:57:26: 1000000 INFO @ Mon, 03 Jun 2019 02:57:26: 1000000 INFO @ Mon, 03 Jun 2019 02:57:29: 1000000 INFO @ Mon, 03 Jun 2019 02:57:34: 2000000 INFO @ Mon, 03 Jun 2019 02:57:35: 2000000 INFO @ Mon, 03 Jun 2019 02:57:40: 2000000 INFO @ Mon, 03 Jun 2019 02:57:43: 3000000 INFO @ Mon, 03 Jun 2019 02:57:43: 3000000 INFO @ Mon, 03 Jun 2019 02:57:50: 4000000 INFO @ Mon, 03 Jun 2019 02:57:51: 3000000 INFO @ Mon, 03 Jun 2019 02:57:51: 4000000 INFO @ Mon, 03 Jun 2019 02:57:57: 5000000 INFO @ Mon, 03 Jun 2019 02:57:59: 5000000 INFO @ Mon, 03 Jun 2019 02:58:02: 4000000 INFO @ Mon, 03 Jun 2019 02:58:04: 6000000 INFO @ Mon, 03 Jun 2019 02:58:07: 6000000 INFO @ Mon, 03 Jun 2019 02:58:12: 7000000 INFO @ Mon, 03 Jun 2019 02:58:12: 5000000 INFO @ Mon, 03 Jun 2019 02:58:15: 7000000 INFO @ Mon, 03 Jun 2019 02:58:19: 8000000 INFO @ Mon, 03 Jun 2019 02:58:21: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:58:21: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:58:21: #1 total tags in treatment: 8276127 INFO @ Mon, 03 Jun 2019 02:58:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:58:21: #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 02:58:21: #1 tags after filtering in treatment: 8276127 INFO @ Mon, 03 Jun 2019 02:58:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:58:21: #1 finished! INFO @ Mon, 03 Jun 2019 02:58:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:58:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:58:22: #2 number of paired peaks: 2011 INFO @ Mon, 03 Jun 2019 02:58:22: start model_add_line... INFO @ Mon, 03 Jun 2019 02:58:22: start X-correlation... INFO @ Mon, 03 Jun 2019 02:58:22: end of X-cor INFO @ Mon, 03 Jun 2019 02:58:22: #2 finished! INFO @ Mon, 03 Jun 2019 02:58:22: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 02:58:22: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 02:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.20_model.r INFO @ Mon, 03 Jun 2019 02:58:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:58:23: 6000000 INFO @ Mon, 03 Jun 2019 02:58:23: 8000000 INFO @ Mon, 03 Jun 2019 02:58:25: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:58:25: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:58:25: #1 total tags in treatment: 8276127 INFO @ Mon, 03 Jun 2019 02:58:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:58:25: #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 02:58:25: #1 tags after filtering in treatment: 8276127 INFO @ Mon, 03 Jun 2019 02:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:58:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:58:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:58:26: #2 number of paired peaks: 2011 INFO @ Mon, 03 Jun 2019 02:58:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:58:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:58:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:58:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:58:26: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 02:58:26: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 02:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.05_model.r INFO @ Mon, 03 Jun 2019 02:58:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:58:33: 7000000 INFO @ Mon, 03 Jun 2019 02:58:43: 8000000 INFO @ Mon, 03 Jun 2019 02:58:46: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:58:46: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:58:46: #1 total tags in treatment: 8276127 INFO @ Mon, 03 Jun 2019 02:58:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:58:46: #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 02:58:46: #1 tags after filtering in treatment: 8276127 INFO @ Mon, 03 Jun 2019 02:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:58:46: #1 finished! INFO @ Mon, 03 Jun 2019 02:58:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:58:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:58:47: #2 number of paired peaks: 2011 INFO @ Mon, 03 Jun 2019 02:58:47: start model_add_line... INFO @ Mon, 03 Jun 2019 02:58:47: start X-correlation... INFO @ Mon, 03 Jun 2019 02:58:47: end of X-cor INFO @ Mon, 03 Jun 2019 02:58:47: #2 finished! INFO @ Mon, 03 Jun 2019 02:58:47: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 02:58:47: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 02:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.10_model.r INFO @ Mon, 03 Jun 2019 02:58:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:58:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.20_summits.bed INFO @ Mon, 03 Jun 2019 02:58:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (800 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.05_summits.bed INFO @ Mon, 03 Jun 2019 02:59:03: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5307 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:59:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299938/SRX1299938.10_summits.bed INFO @ Mon, 03 Jun 2019 02:59:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2420 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。