Job ID = 1300859 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:28:47 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 ) 2019-06-03T10:28:47 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 ) 2019-06-03T10:34:03 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 ) 2019-06-03T10:37:08 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 : 30,386,029 reads read : 30,386,029 reads written : 30,386,029 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: 00:07:26 30386029 reads; of these: 30386029 (100.00%) were unpaired; of these: 14086006 (46.36%) aligned 0 times 12242110 (40.29%) aligned exactly 1 time 4057913 (13.35%) aligned >1 times 53.64% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 7828990 / 16300023 = 0.4803 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 19:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.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 19:49:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:49:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.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 19:49:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:49:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.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 19:49:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:49:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:49:38: 1000000 INFO @ Mon, 03 Jun 2019 19:49:41: 1000000 INFO @ Mon, 03 Jun 2019 19:49:41: 1000000 INFO @ Mon, 03 Jun 2019 19:49:47: 2000000 INFO @ Mon, 03 Jun 2019 19:49:52: 2000000 INFO @ Mon, 03 Jun 2019 19:49:52: 2000000 INFO @ Mon, 03 Jun 2019 19:49:55: 3000000 INFO @ Mon, 03 Jun 2019 19:50:03: 3000000 INFO @ Mon, 03 Jun 2019 19:50:03: 3000000 INFO @ Mon, 03 Jun 2019 19:50:03: 4000000 INFO @ Mon, 03 Jun 2019 19:50:12: 5000000 INFO @ Mon, 03 Jun 2019 19:50:14: 4000000 INFO @ Mon, 03 Jun 2019 19:50:14: 4000000 INFO @ Mon, 03 Jun 2019 19:50:21: 6000000 INFO @ Mon, 03 Jun 2019 19:50:24: 5000000 INFO @ Mon, 03 Jun 2019 19:50:25: 5000000 INFO @ Mon, 03 Jun 2019 19:50:29: 7000000 INFO @ Mon, 03 Jun 2019 19:50:35: 6000000 INFO @ Mon, 03 Jun 2019 19:50:35: 6000000 INFO @ Mon, 03 Jun 2019 19:50:37: 8000000 INFO @ Mon, 03 Jun 2019 19:50:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:50:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:50:40: #1 total tags in treatment: 8471033 INFO @ Mon, 03 Jun 2019 19:50:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:50:40: #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 19:50:41: #1 tags after filtering in treatment: 8471033 INFO @ Mon, 03 Jun 2019 19:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:50:41: #1 finished! INFO @ Mon, 03 Jun 2019 19:50:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:50:42: #2 number of paired peaks: 3857 INFO @ Mon, 03 Jun 2019 19:50:42: start model_add_line... INFO @ Mon, 03 Jun 2019 19:50:42: start X-correlation... INFO @ Mon, 03 Jun 2019 19:50:42: end of X-cor INFO @ Mon, 03 Jun 2019 19:50:42: #2 finished! INFO @ Mon, 03 Jun 2019 19:50:42: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 19:50:42: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 19:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.10_model.r INFO @ Mon, 03 Jun 2019 19:50:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:50:45: 7000000 INFO @ Mon, 03 Jun 2019 19:50:45: 7000000 INFO @ Mon, 03 Jun 2019 19:50:56: 8000000 INFO @ Mon, 03 Jun 2019 19:50:56: 8000000 INFO @ Mon, 03 Jun 2019 19:51:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:00: #1 total tags in treatment: 8471033 INFO @ Mon, 03 Jun 2019 19:51:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:00: #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 19:51:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:00: #1 total tags in treatment: 8471033 INFO @ Mon, 03 Jun 2019 19:51:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:00: #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 19:51:00: #1 tags after filtering in treatment: 8471033 INFO @ Mon, 03 Jun 2019 19:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:51:00: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:01: #1 tags after filtering in treatment: 8471033 INFO @ Mon, 03 Jun 2019 19:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:51:01: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:02: #2 number of paired peaks: 3857 INFO @ Mon, 03 Jun 2019 19:51:02: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:02: #2 number of paired peaks: 3857 INFO @ Mon, 03 Jun 2019 19:51:02: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:02: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:02: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:02: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:02: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 19:51:02: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 19:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.20_model.r INFO @ Mon, 03 Jun 2019 19:51:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:02: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:02: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:02: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:02: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 19:51:02: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 19:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.05_model.r INFO @ Mon, 03 Jun 2019 19:51:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:51:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:51:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:51:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.10_summits.bed INFO @ Mon, 03 Jun 2019 19:51:26: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6685 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:51:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:51:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.05_summits.bed INFO @ Mon, 03 Jun 2019 19:51:45: Done! INFO @ Mon, 03 Jun 2019 19:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.20_peaks.narrowPeak pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7897 records, 4 fields): 14 millis INFO @ Mon, 03 Jun 2019 19:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823795/SRX4823795.20_summits.bed CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:51:45: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5275 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。