Job ID = 1300308 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:14:35 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 ) 2019-06-03T10:14:35 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 ) 2019-06-03T10:14:35 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 ) 2019-06-03T10:14:38 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 ) 2019-06-03T10:14:38 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 : 13,900,069 reads read : 13,900,069 reads written : 13,900,069 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: 00:04:33 13900069 reads; of these: 13900069 (100.00%) were unpaired; of these: 562341 (4.05%) aligned 0 times 11463161 (82.47%) aligned exactly 1 time 1874567 (13.49%) aligned >1 times 95.95% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 3866740 / 13337728 = 0.2899 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 19:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.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 19:26:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:26:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.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 19:26:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:26:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.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 19:26:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:26:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:26:14: 1000000 INFO @ Mon, 03 Jun 2019 19:26:15: 1000000 INFO @ Mon, 03 Jun 2019 19:26:16: 1000000 INFO @ Mon, 03 Jun 2019 19:26:22: 2000000 INFO @ Mon, 03 Jun 2019 19:26:24: 2000000 INFO @ Mon, 03 Jun 2019 19:26:26: 2000000 INFO @ Mon, 03 Jun 2019 19:26:30: 3000000 INFO @ Mon, 03 Jun 2019 19:26:32: 3000000 INFO @ Mon, 03 Jun 2019 19:26:35: 3000000 INFO @ Mon, 03 Jun 2019 19:26:37: 4000000 INFO @ Mon, 03 Jun 2019 19:26:41: 4000000 INFO @ Mon, 03 Jun 2019 19:26:45: 4000000 INFO @ Mon, 03 Jun 2019 19:26:45: 5000000 INFO @ Mon, 03 Jun 2019 19:26:50: 5000000 INFO @ Mon, 03 Jun 2019 19:26:52: 6000000 INFO @ Mon, 03 Jun 2019 19:26:53: 5000000 INFO @ Mon, 03 Jun 2019 19:26:59: 6000000 INFO @ Mon, 03 Jun 2019 19:27:00: 7000000 INFO @ Mon, 03 Jun 2019 19:27:02: 6000000 INFO @ Mon, 03 Jun 2019 19:27:07: 7000000 INFO @ Mon, 03 Jun 2019 19:27:07: 8000000 INFO @ Mon, 03 Jun 2019 19:27:10: 7000000 INFO @ Mon, 03 Jun 2019 19:27:15: 9000000 INFO @ Mon, 03 Jun 2019 19:27:16: 8000000 INFO @ Mon, 03 Jun 2019 19:27:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:27:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:27:18: #1 total tags in treatment: 9470988 INFO @ Mon, 03 Jun 2019 19:27:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:27:18: #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 19:27:19: #1 tags after filtering in treatment: 9470988 INFO @ Mon, 03 Jun 2019 19:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:27:19: #1 finished! INFO @ Mon, 03 Jun 2019 19:27:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:27:19: 8000000 INFO @ Mon, 03 Jun 2019 19:27:20: #2 number of paired peaks: 9144 INFO @ Mon, 03 Jun 2019 19:27:20: start model_add_line... INFO @ Mon, 03 Jun 2019 19:27:20: start X-correlation... INFO @ Mon, 03 Jun 2019 19:27:21: end of X-cor INFO @ Mon, 03 Jun 2019 19:27:21: #2 finished! INFO @ Mon, 03 Jun 2019 19:27:21: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 19:27:21: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 19:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.10_model.r INFO @ Mon, 03 Jun 2019 19:27:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:27:25: 9000000 INFO @ Mon, 03 Jun 2019 19:27:27: 9000000 INFO @ Mon, 03 Jun 2019 19:27:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:27:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:27:29: #1 total tags in treatment: 9470988 INFO @ Mon, 03 Jun 2019 19:27:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:27:29: #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 19:27:29: #1 tags after filtering in treatment: 9470988 INFO @ Mon, 03 Jun 2019 19:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:27:29: #1 finished! INFO @ Mon, 03 Jun 2019 19:27:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:27:31: #2 number of paired peaks: 9144 INFO @ Mon, 03 Jun 2019 19:27:31: start model_add_line... INFO @ Mon, 03 Jun 2019 19:27:31: start X-correlation... INFO @ Mon, 03 Jun 2019 19:27:31: end of X-cor INFO @ Mon, 03 Jun 2019 19:27:31: #2 finished! INFO @ Mon, 03 Jun 2019 19:27:31: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 19:27:31: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 19:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.05_model.r INFO @ Mon, 03 Jun 2019 19:27:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:27:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:27:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:27:31: #1 total tags in treatment: 9470988 INFO @ Mon, 03 Jun 2019 19:27:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:27:31: #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 19:27:32: #1 tags after filtering in treatment: 9470988 INFO @ Mon, 03 Jun 2019 19:27:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:27:32: #1 finished! INFO @ Mon, 03 Jun 2019 19:27:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:27:33: #2 number of paired peaks: 9144 INFO @ Mon, 03 Jun 2019 19:27:33: start model_add_line... INFO @ Mon, 03 Jun 2019 19:27:34: start X-correlation... INFO @ Mon, 03 Jun 2019 19:27:34: end of X-cor INFO @ Mon, 03 Jun 2019 19:27:34: #2 finished! INFO @ Mon, 03 Jun 2019 19:27:34: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 19:27:34: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 19:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.20_model.r INFO @ Mon, 03 Jun 2019 19:27:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:27:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:28:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:28:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.10_summits.bed INFO @ Mon, 03 Jun 2019 19:28:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7600 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:28:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.05_summits.bed INFO @ Mon, 03 Jun 2019 19:28:18: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8590 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481093/SRX481093.20_summits.bed INFO @ Mon, 03 Jun 2019 19:28:19: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6257 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。