Job ID = 1293617 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T15:59:40 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 ) 2019-06-02T15:59:40 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 ) 2019-06-02T15:59:40 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 ) 2019-06-02T15:59:40 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 : 24,535,827 reads read : 24,535,827 reads written : 24,535,827 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: 00:09:06 24535827 reads; of these: 24535827 (100.00%) were unpaired; of these: 759754 (3.10%) aligned 0 times 19343961 (78.84%) aligned exactly 1 time 4432112 (18.06%) aligned >1 times 96.90% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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_rmdupse_core] 4941928 / 23776073 = 0.2079 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 01:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.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 01:16:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:16:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.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 01:16:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:16:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.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 01:16:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:16:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:16:53: 1000000 INFO @ Mon, 03 Jun 2019 01:16:54: 1000000 INFO @ Mon, 03 Jun 2019 01:16:54: 1000000 INFO @ Mon, 03 Jun 2019 01:17:03: 2000000 INFO @ Mon, 03 Jun 2019 01:17:05: 2000000 INFO @ Mon, 03 Jun 2019 01:17:05: 2000000 INFO @ Mon, 03 Jun 2019 01:17:14: 3000000 INFO @ Mon, 03 Jun 2019 01:17:14: 3000000 INFO @ Mon, 03 Jun 2019 01:17:14: 3000000 INFO @ Mon, 03 Jun 2019 01:17:24: 4000000 INFO @ Mon, 03 Jun 2019 01:17:24: 4000000 INFO @ Mon, 03 Jun 2019 01:17:25: 4000000 INFO @ Mon, 03 Jun 2019 01:17:34: 5000000 INFO @ Mon, 03 Jun 2019 01:17:34: 5000000 INFO @ Mon, 03 Jun 2019 01:17:36: 5000000 INFO @ Mon, 03 Jun 2019 01:17:43: 6000000 INFO @ Mon, 03 Jun 2019 01:17:43: 6000000 INFO @ Mon, 03 Jun 2019 01:17:46: 6000000 INFO @ Mon, 03 Jun 2019 01:17:52: 7000000 INFO @ Mon, 03 Jun 2019 01:17:52: 7000000 INFO @ Mon, 03 Jun 2019 01:17:56: 7000000 INFO @ Mon, 03 Jun 2019 01:18:02: 8000000 INFO @ Mon, 03 Jun 2019 01:18:02: 8000000 INFO @ Mon, 03 Jun 2019 01:18:07: 8000000 INFO @ Mon, 03 Jun 2019 01:18:11: 9000000 INFO @ Mon, 03 Jun 2019 01:18:11: 9000000 INFO @ Mon, 03 Jun 2019 01:18:17: 9000000 INFO @ Mon, 03 Jun 2019 01:18:20: 10000000 INFO @ Mon, 03 Jun 2019 01:18:20: 10000000 INFO @ Mon, 03 Jun 2019 01:18:27: 10000000 INFO @ Mon, 03 Jun 2019 01:18:29: 11000000 INFO @ Mon, 03 Jun 2019 01:18:29: 11000000 INFO @ Mon, 03 Jun 2019 01:18:37: 11000000 INFO @ Mon, 03 Jun 2019 01:18:38: 12000000 INFO @ Mon, 03 Jun 2019 01:18:38: 12000000 INFO @ Mon, 03 Jun 2019 01:18:47: 13000000 INFO @ Mon, 03 Jun 2019 01:18:47: 13000000 INFO @ Mon, 03 Jun 2019 01:18:48: 12000000 INFO @ Mon, 03 Jun 2019 01:18:56: 14000000 INFO @ Mon, 03 Jun 2019 01:18:56: 14000000 INFO @ Mon, 03 Jun 2019 01:18:59: 13000000 INFO @ Mon, 03 Jun 2019 01:19:05: 15000000 INFO @ Mon, 03 Jun 2019 01:19:05: 15000000 INFO @ Mon, 03 Jun 2019 01:19:09: 14000000 INFO @ Mon, 03 Jun 2019 01:19:14: 16000000 INFO @ Mon, 03 Jun 2019 01:19:15: 16000000 INFO @ Mon, 03 Jun 2019 01:19:20: 15000000 INFO @ Mon, 03 Jun 2019 01:19:23: 17000000 INFO @ Mon, 03 Jun 2019 01:19:24: 17000000 INFO @ Mon, 03 Jun 2019 01:19:30: 16000000 INFO @ Mon, 03 Jun 2019 01:19:33: 18000000 INFO @ Mon, 03 Jun 2019 01:19:33: 18000000 INFO @ Mon, 03 Jun 2019 01:19:40: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:19:40: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:19:40: #1 total tags in treatment: 18834145 INFO @ Mon, 03 Jun 2019 01:19:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:19:40: #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 01:19:41: 17000000 INFO @ Mon, 03 Jun 2019 01:19:41: #1 tags after filtering in treatment: 18834145 INFO @ Mon, 03 Jun 2019 01:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:19:41: #1 finished! INFO @ Mon, 03 Jun 2019 01:19:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:19:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:19:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:19:41: #1 total tags in treatment: 18834145 INFO @ Mon, 03 Jun 2019 01:19:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:19:41: #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 01:19:41: #1 tags after filtering in treatment: 18834145 INFO @ Mon, 03 Jun 2019 01:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:19:41: #1 finished! INFO @ Mon, 03 Jun 2019 01:19:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:19:43: #2 number of paired peaks: 4454 INFO @ Mon, 03 Jun 2019 01:19:43: start model_add_line... INFO @ Mon, 03 Jun 2019 01:19:43: start X-correlation... INFO @ Mon, 03 Jun 2019 01:19:43: end of X-cor INFO @ Mon, 03 Jun 2019 01:19:43: #2 finished! INFO @ Mon, 03 Jun 2019 01:19:43: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 01:19:43: #2 alternative fragment length(s) may be 4,145 bps INFO @ Mon, 03 Jun 2019 01:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.20_model.r INFO @ Mon, 03 Jun 2019 01:19:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:19:43: #2 number of paired peaks: 4454 INFO @ Mon, 03 Jun 2019 01:19:43: start model_add_line... INFO @ Mon, 03 Jun 2019 01:19:44: start X-correlation... INFO @ Mon, 03 Jun 2019 01:19:44: end of X-cor INFO @ Mon, 03 Jun 2019 01:19:44: #2 finished! INFO @ Mon, 03 Jun 2019 01:19:44: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 01:19:44: #2 alternative fragment length(s) may be 4,145 bps INFO @ Mon, 03 Jun 2019 01:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.10_model.r INFO @ Mon, 03 Jun 2019 01:19:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:19:50: 18000000 INFO @ Mon, 03 Jun 2019 01:19:59: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:19:59: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:19:59: #1 total tags in treatment: 18834145 INFO @ Mon, 03 Jun 2019 01:19:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:19:59: #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 01:19:59: #1 tags after filtering in treatment: 18834145 INFO @ Mon, 03 Jun 2019 01:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:19:59: #1 finished! INFO @ Mon, 03 Jun 2019 01:19:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:20:01: #2 number of paired peaks: 4454 INFO @ Mon, 03 Jun 2019 01:20:01: start model_add_line... INFO @ Mon, 03 Jun 2019 01:20:01: start X-correlation... INFO @ Mon, 03 Jun 2019 01:20:01: end of X-cor INFO @ Mon, 03 Jun 2019 01:20:01: #2 finished! INFO @ Mon, 03 Jun 2019 01:20:01: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 01:20:01: #2 alternative fragment length(s) may be 4,145 bps INFO @ Mon, 03 Jun 2019 01:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.05_model.r INFO @ Mon, 03 Jun 2019 01:20:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:20:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:20:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:21:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.20_summits.bed INFO @ Mon, 03 Jun 2019 01:21:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (745 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.10_summits.bed INFO @ Mon, 03 Jun 2019 01:21:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2110 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:21:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032393/SRX1032393.05_summits.bed INFO @ Mon, 03 Jun 2019 01:21:24: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5080 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。