Job ID = 4178513 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:38:27 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 ) 1900-01-00T00:00:00 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 ) 2019-12-05T03:41:38 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 ) 2019-12-05T03:41:38 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 ) 2019-12-05T03:44:05 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 : 22,287,048 reads read : 22,287,048 reads written : 22,287,048 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:39 22287048 reads; of these: 22287048 (100.00%) were unpaired; of these: 2619585 (11.75%) aligned 0 times 15471239 (69.42%) aligned exactly 1 time 4196224 (18.83%) aligned >1 times 88.25% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 6921728 / 19667463 = 0.3519 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.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 @ Thu, 05 Dec 2019 12:55:17: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:55:17: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:55:24: 1000000 INFO @ Thu, 05 Dec 2019 12:55:32: 2000000 INFO @ Thu, 05 Dec 2019 12:55:39: 3000000 INFO @ Thu, 05 Dec 2019 12:55:46: 4000000 INFO @ Thu, 05 Dec 2019 12:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.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 @ Thu, 05 Dec 2019 12:55:47: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:55:47: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:55:54: 5000000 INFO @ Thu, 05 Dec 2019 12:55:55: 1000000 INFO @ Thu, 05 Dec 2019 12:56:01: 6000000 INFO @ Thu, 05 Dec 2019 12:56:02: 2000000 INFO @ Thu, 05 Dec 2019 12:56:09: 7000000 INFO @ Thu, 05 Dec 2019 12:56:09: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:56:17: 8000000 INFO @ Thu, 05 Dec 2019 12:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.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 @ Thu, 05 Dec 2019 12:56:17: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:17: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:17: 4000000 INFO @ Thu, 05 Dec 2019 12:56:23: 1000000 INFO @ Thu, 05 Dec 2019 12:56:24: 9000000 INFO @ Thu, 05 Dec 2019 12:56:25: 5000000 INFO @ Thu, 05 Dec 2019 12:56:29: 2000000 INFO @ Thu, 05 Dec 2019 12:56:32: 10000000 INFO @ Thu, 05 Dec 2019 12:56:32: 6000000 INFO @ Thu, 05 Dec 2019 12:56:35: 3000000 INFO @ Thu, 05 Dec 2019 12:56:40: 11000000 INFO @ Thu, 05 Dec 2019 12:56:40: 7000000 INFO @ Thu, 05 Dec 2019 12:56:41: 4000000 INFO @ Thu, 05 Dec 2019 12:56:47: 12000000 INFO @ Thu, 05 Dec 2019 12:56:47: 8000000 INFO @ Thu, 05 Dec 2019 12:56:47: 5000000 INFO @ Thu, 05 Dec 2019 12:56:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:56:53: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:56:53: #1 total tags in treatment: 12745735 INFO @ Thu, 05 Dec 2019 12:56:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:56:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:56:53: #1 tags after filtering in treatment: 12745735 INFO @ Thu, 05 Dec 2019 12:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:56:53: #1 finished! INFO @ Thu, 05 Dec 2019 12:56:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:56:53: 6000000 INFO @ Thu, 05 Dec 2019 12:56:54: #2 number of paired peaks: 2162 INFO @ Thu, 05 Dec 2019 12:56:54: start model_add_line... INFO @ Thu, 05 Dec 2019 12:56:54: start X-correlation... INFO @ Thu, 05 Dec 2019 12:56:54: end of X-cor INFO @ Thu, 05 Dec 2019 12:56:54: #2 finished! INFO @ Thu, 05 Dec 2019 12:56:54: #2 predicted fragment length is 149 bps INFO @ Thu, 05 Dec 2019 12:56:54: #2 alternative fragment length(s) may be 22,59,111,136,149,245 bps INFO @ Thu, 05 Dec 2019 12:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.05_model.r INFO @ Thu, 05 Dec 2019 12:56:54: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:56:55: 9000000 INFO @ Thu, 05 Dec 2019 12:56:59: 7000000 INFO @ Thu, 05 Dec 2019 12:57:02: 10000000 INFO @ Thu, 05 Dec 2019 12:57:05: 8000000 INFO @ Thu, 05 Dec 2019 12:57:09: 11000000 INFO @ Thu, 05 Dec 2019 12:57:11: 9000000 INFO @ Thu, 05 Dec 2019 12:57:16: 12000000 INFO @ Thu, 05 Dec 2019 12:57:17: 10000000 INFO @ Thu, 05 Dec 2019 12:57:21: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:57:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:57:22: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:57:22: #1 total tags in treatment: 12745735 INFO @ Thu, 05 Dec 2019 12:57:22: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:57:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:57:22: #1 tags after filtering in treatment: 12745735 INFO @ Thu, 05 Dec 2019 12:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:57:22: #1 finished! INFO @ Thu, 05 Dec 2019 12:57:22: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:57:23: 11000000 INFO @ Thu, 05 Dec 2019 12:57:23: #2 number of paired peaks: 2162 INFO @ Thu, 05 Dec 2019 12:57:23: start model_add_line... INFO @ Thu, 05 Dec 2019 12:57:23: start X-correlation... INFO @ Thu, 05 Dec 2019 12:57:23: end of X-cor INFO @ Thu, 05 Dec 2019 12:57:23: #2 finished! INFO @ Thu, 05 Dec 2019 12:57:23: #2 predicted fragment length is 149 bps INFO @ Thu, 05 Dec 2019 12:57:23: #2 alternative fragment length(s) may be 22,59,111,136,149,245 bps INFO @ Thu, 05 Dec 2019 12:57:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.10_model.r INFO @ Thu, 05 Dec 2019 12:57:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:57:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:57:29: 12000000 INFO @ Thu, 05 Dec 2019 12:57:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:57:33: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:57:33: #1 total tags in treatment: 12745735 INFO @ Thu, 05 Dec 2019 12:57:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:57:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:57:33: #1 tags after filtering in treatment: 12745735 INFO @ Thu, 05 Dec 2019 12:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:57:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:57:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:57:34: #2 number of paired peaks: 2162 INFO @ Thu, 05 Dec 2019 12:57:34: start model_add_line... INFO @ Thu, 05 Dec 2019 12:57:34: start X-correlation... INFO @ Thu, 05 Dec 2019 12:57:34: end of X-cor INFO @ Thu, 05 Dec 2019 12:57:34: #2 finished! INFO @ Thu, 05 Dec 2019 12:57:34: #2 predicted fragment length is 149 bps INFO @ Thu, 05 Dec 2019 12:57:34: #2 alternative fragment length(s) may be 22,59,111,136,149,245 bps INFO @ Thu, 05 Dec 2019 12:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.20_model.r INFO @ Thu, 05 Dec 2019 12:57:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.05_summits.bed INFO @ Thu, 05 Dec 2019 12:57:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2876 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:57:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:01: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.10_summits.bed INFO @ Thu, 05 Dec 2019 12:58:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1209 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717035/SRX5717035.20_summits.bed INFO @ Thu, 05 Dec 2019 12:58:16: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (507 records, 4 fields): 53 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。