Job ID = 1293797 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:24:04 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 ) 2019-06-02T17:24:04 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 ) 2019-06-02T17:24:43 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 ) 2019-06-02T17:24:43 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( ) 2019-06-02T17:24:43 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 ) 2019-06-02T17:24:43 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 ) 2019-06-02T17:24:54 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 ) 2019-06-02T17:25:03 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 ) 2019-06-02T17:27:16 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 ) 2019-06-02T17:27:32 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 ) 2019-06-02T17:33:59 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 ) 2019-06-02T17:33:59 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 : 19,431,754 reads read : 19,431,754 reads written : 19,431,754 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: 00:05:34 19431754 reads; of these: 19431754 (100.00%) were unpaired; of these: 1891572 (9.73%) aligned 0 times 15345287 (78.97%) aligned exactly 1 time 2194895 (11.30%) aligned >1 times 90.27% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 9253761 / 17540182 = 0.5276 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 02:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.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 02:45:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:45:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.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 02:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.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 02:45:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:45:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:45:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:45:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:45:26: 1000000 INFO @ Mon, 03 Jun 2019 02:45:27: 1000000 INFO @ Mon, 03 Jun 2019 02:45:27: 1000000 INFO @ Mon, 03 Jun 2019 02:45:34: 2000000 INFO @ Mon, 03 Jun 2019 02:45:35: 2000000 INFO @ Mon, 03 Jun 2019 02:45:36: 2000000 INFO @ Mon, 03 Jun 2019 02:45:42: 3000000 INFO @ Mon, 03 Jun 2019 02:45:43: 3000000 INFO @ Mon, 03 Jun 2019 02:45:44: 3000000 INFO @ Mon, 03 Jun 2019 02:45:50: 4000000 INFO @ Mon, 03 Jun 2019 02:45:51: 4000000 INFO @ Mon, 03 Jun 2019 02:45:53: 4000000 INFO @ Mon, 03 Jun 2019 02:45:58: 5000000 INFO @ Mon, 03 Jun 2019 02:45:58: 5000000 INFO @ Mon, 03 Jun 2019 02:46:02: 5000000 INFO @ Mon, 03 Jun 2019 02:46:06: 6000000 INFO @ Mon, 03 Jun 2019 02:46:06: 6000000 INFO @ Mon, 03 Jun 2019 02:46:10: 6000000 INFO @ Mon, 03 Jun 2019 02:46:14: 7000000 INFO @ Mon, 03 Jun 2019 02:46:15: 7000000 INFO @ Mon, 03 Jun 2019 02:46:19: 7000000 INFO @ Mon, 03 Jun 2019 02:46:22: 8000000 INFO @ Mon, 03 Jun 2019 02:46:23: 8000000 INFO @ Mon, 03 Jun 2019 02:46:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:25: #1 total tags in treatment: 8286421 INFO @ Mon, 03 Jun 2019 02:46:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:25: #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 02:46:25: #1 tags after filtering in treatment: 8286421 INFO @ Mon, 03 Jun 2019 02:46:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:25: #1 total tags in treatment: 8286421 INFO @ Mon, 03 Jun 2019 02:46:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:25: #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 02:46:25: #1 tags after filtering in treatment: 8286421 INFO @ Mon, 03 Jun 2019 02:46:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:26: #2 number of paired peaks: 3465 INFO @ Mon, 03 Jun 2019 02:46:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:26: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 02:46:26: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 02:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.10_model.r INFO @ Mon, 03 Jun 2019 02:46:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:26: #2 number of paired peaks: 3465 INFO @ Mon, 03 Jun 2019 02:46:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:26: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 02:46:26: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 02:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.05_model.r INFO @ Mon, 03 Jun 2019 02:46:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:27: 8000000 INFO @ Mon, 03 Jun 2019 02:46:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:30: #1 total tags in treatment: 8286421 INFO @ Mon, 03 Jun 2019 02:46:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:30: #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 02:46:30: #1 tags after filtering in treatment: 8286421 INFO @ Mon, 03 Jun 2019 02:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:30: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:31: #2 number of paired peaks: 3465 INFO @ Mon, 03 Jun 2019 02:46:31: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:31: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:31: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:31: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:31: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 02:46:31: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 02:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.20_model.r INFO @ Mon, 03 Jun 2019 02:46:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:47:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.10_summits.bed INFO @ Mon, 03 Jun 2019 02:47:10: Done! INFO @ Mon, 03 Jun 2019 02:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.05_peaks.xls pass1 - making usageList (13 chroms): 2 millis INFO @ Mon, 03 Jun 2019 02:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.05_peaks.narrowPeak pass2 - checking and writing primary data (4045 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.05_summits.bed INFO @ Mon, 03 Jun 2019 02:47:10: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5371 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134698/SRX1134698.20_summits.bed INFO @ Mon, 03 Jun 2019 02:47:15: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2886 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。