Job ID = 1307944 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:35:15 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 ) 2019-06-03T13:35:15 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 ) 2019-06-03T13:35:15 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 ) 2019-06-03T13:43:33 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 ) 2019-06-03T13:35:15 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 : 28,096,914 reads read : 56,193,828 reads written : 28,096,914 reads 0-length : 28,096,914 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: 00:08:43 28096914 reads; of these: 28096914 (100.00%) were unpaired; of these: 9926917 (35.33%) aligned 0 times 15891377 (56.56%) aligned exactly 1 time 2278620 (8.11%) aligned >1 times 64.67% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 15045503 / 18169997 = 0.8280 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 22:57:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.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 22:57:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.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 22:57:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.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 22:57:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:22: 1000000 INFO @ Mon, 03 Jun 2019 22:57:23: 1000000 INFO @ Mon, 03 Jun 2019 22:57:23: 1000000 INFO @ Mon, 03 Jun 2019 22:57:32: 2000000 INFO @ Mon, 03 Jun 2019 22:57:34: 2000000 INFO @ Mon, 03 Jun 2019 22:57:34: 2000000 INFO @ Mon, 03 Jun 2019 22:57:42: 3000000 INFO @ Mon, 03 Jun 2019 22:57:43: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:57:43: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:57:43: #1 total tags in treatment: 3124494 INFO @ Mon, 03 Jun 2019 22:57:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:57:43: #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 22:57:43: #1 tags after filtering in treatment: 3124494 INFO @ Mon, 03 Jun 2019 22:57:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:57:43: #1 finished! INFO @ Mon, 03 Jun 2019 22:57:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:57:44: #2 number of paired peaks: 7635 INFO @ Mon, 03 Jun 2019 22:57:44: start model_add_line... INFO @ Mon, 03 Jun 2019 22:57:44: start X-correlation... INFO @ Mon, 03 Jun 2019 22:57:44: end of X-cor INFO @ Mon, 03 Jun 2019 22:57:44: #2 finished! INFO @ Mon, 03 Jun 2019 22:57:44: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 22:57:44: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 22:57:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.10_model.r INFO @ Mon, 03 Jun 2019 22:57:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:57:46: 3000000 INFO @ Mon, 03 Jun 2019 22:57:46: 3000000 INFO @ Mon, 03 Jun 2019 22:57:47: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:57:47: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:57:47: #1 total tags in treatment: 3124494 INFO @ Mon, 03 Jun 2019 22:57:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:57:47: #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 22:57:47: #1 tags after filtering in treatment: 3124494 INFO @ Mon, 03 Jun 2019 22:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:57:47: #1 finished! INFO @ Mon, 03 Jun 2019 22:57:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:57:47: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:57:47: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:57:47: #1 total tags in treatment: 3124494 INFO @ Mon, 03 Jun 2019 22:57:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:57:47: #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 22:57:47: #1 tags after filtering in treatment: 3124494 INFO @ Mon, 03 Jun 2019 22:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:57:47: #1 finished! INFO @ Mon, 03 Jun 2019 22:57:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:57:47: #2 number of paired peaks: 7635 INFO @ Mon, 03 Jun 2019 22:57:47: start model_add_line... INFO @ Mon, 03 Jun 2019 22:57:48: start X-correlation... INFO @ Mon, 03 Jun 2019 22:57:48: end of X-cor INFO @ Mon, 03 Jun 2019 22:57:48: #2 finished! INFO @ Mon, 03 Jun 2019 22:57:48: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 22:57:48: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 22:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.20_model.r INFO @ Mon, 03 Jun 2019 22:57:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:57:48: #2 number of paired peaks: 7635 INFO @ Mon, 03 Jun 2019 22:57:48: start model_add_line... INFO @ Mon, 03 Jun 2019 22:57:48: start X-correlation... INFO @ Mon, 03 Jun 2019 22:57:48: end of X-cor INFO @ Mon, 03 Jun 2019 22:57:48: #2 finished! INFO @ Mon, 03 Jun 2019 22:57:48: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 22:57:48: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 22:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.05_model.r INFO @ Mon, 03 Jun 2019 22:57:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:57:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:57:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:58:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.10_summits.bed INFO @ Mon, 03 Jun 2019 22:58:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5574 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.05_summits.bed INFO @ Mon, 03 Jun 2019 22:58:05: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7390 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343124/SRX5343124.20_summits.bed INFO @ Mon, 03 Jun 2019 22:58:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2746 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。