Job ID = 1297407 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:04:50 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 ) 2019-06-03T08:04:50 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 : 52,246,525 reads read : 104,493,050 reads written : 104,493,050 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:44 52246525 reads; of these: 52246525 (100.00%) were paired; of these: 48966992 (93.72%) aligned concordantly 0 times 2587421 (4.95%) aligned concordantly exactly 1 time 692112 (1.32%) aligned concordantly >1 times ---- 48966992 pairs aligned concordantly 0 times; of these: 6774 (0.01%) aligned discordantly 1 time ---- 48960218 pairs aligned 0 times concordantly or discordantly; of these: 97920436 mates make up the pairs; of these: 97261958 (99.33%) aligned 0 times 280655 (0.29%) aligned exactly 1 time 377823 (0.39%) aligned >1 times 6.92% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 214154 / 3281897 = 0.0653 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 17:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.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 17:30:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:30:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.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 17:30:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:30:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.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 17:30:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:30:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:31:02: 1000000 INFO @ Mon, 03 Jun 2019 17:31:03: 1000000 INFO @ Mon, 03 Jun 2019 17:31:03: 1000000 INFO @ Mon, 03 Jun 2019 17:31:09: 2000000 INFO @ Mon, 03 Jun 2019 17:31:12: 2000000 INFO @ Mon, 03 Jun 2019 17:31:13: 2000000 INFO @ Mon, 03 Jun 2019 17:31:16: 3000000 INFO @ Mon, 03 Jun 2019 17:31:21: 3000000 INFO @ Mon, 03 Jun 2019 17:31:22: 3000000 INFO @ Mon, 03 Jun 2019 17:31:23: 4000000 INFO @ Mon, 03 Jun 2019 17:31:29: 4000000 INFO @ Mon, 03 Jun 2019 17:31:30: 5000000 INFO @ Mon, 03 Jun 2019 17:31:31: 4000000 INFO @ Mon, 03 Jun 2019 17:31:37: 6000000 INFO @ Mon, 03 Jun 2019 17:31:38: 5000000 INFO @ Mon, 03 Jun 2019 17:31:40: 5000000 INFO @ Mon, 03 Jun 2019 17:31:43: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:31:43: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:31:43: #1 total tags in treatment: 3065594 INFO @ Mon, 03 Jun 2019 17:31:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:31:43: #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 17:31:43: #1 tags after filtering in treatment: 2893596 INFO @ Mon, 03 Jun 2019 17:31:43: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 17:31:43: #1 finished! INFO @ Mon, 03 Jun 2019 17:31:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:31:43: #2 number of paired peaks: 1670 INFO @ Mon, 03 Jun 2019 17:31:43: start model_add_line... INFO @ Mon, 03 Jun 2019 17:31:43: start X-correlation... INFO @ Mon, 03 Jun 2019 17:31:44: end of X-cor INFO @ Mon, 03 Jun 2019 17:31:44: #2 finished! INFO @ Mon, 03 Jun 2019 17:31:44: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 17:31:44: #2 alternative fragment length(s) may be 3,144 bps INFO @ Mon, 03 Jun 2019 17:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.10_model.r INFO @ Mon, 03 Jun 2019 17:31:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:31:46: 6000000 INFO @ Mon, 03 Jun 2019 17:31:49: 6000000 INFO @ Mon, 03 Jun 2019 17:31:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:31:53: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:31:53: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:31:53: #1 total tags in treatment: 3065594 INFO @ Mon, 03 Jun 2019 17:31:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:31:53: #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 17:31:53: #1 tags after filtering in treatment: 2893596 INFO @ Mon, 03 Jun 2019 17:31:53: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 17:31:53: #1 finished! INFO @ Mon, 03 Jun 2019 17:31:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:31:53: #2 number of paired peaks: 1670 INFO @ Mon, 03 Jun 2019 17:31:53: start model_add_line... INFO @ Mon, 03 Jun 2019 17:31:53: start X-correlation... INFO @ Mon, 03 Jun 2019 17:31:53: end of X-cor INFO @ Mon, 03 Jun 2019 17:31:53: #2 finished! INFO @ Mon, 03 Jun 2019 17:31:53: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 17:31:53: #2 alternative fragment length(s) may be 3,144 bps INFO @ Mon, 03 Jun 2019 17:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.20_model.r INFO @ Mon, 03 Jun 2019 17:31:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:31:56: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:31:56: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:31:56: #1 total tags in treatment: 3065594 INFO @ Mon, 03 Jun 2019 17:31:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:31:56: #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 17:31:56: #1 tags after filtering in treatment: 2893596 INFO @ Mon, 03 Jun 2019 17:31:56: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 03 Jun 2019 17:31:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:31:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:31:56: #2 number of paired peaks: 1670 INFO @ Mon, 03 Jun 2019 17:31:56: start model_add_line... INFO @ Mon, 03 Jun 2019 17:31:56: start X-correlation... INFO @ Mon, 03 Jun 2019 17:31:56: end of X-cor INFO @ Mon, 03 Jun 2019 17:31:56: #2 finished! INFO @ Mon, 03 Jun 2019 17:31:56: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 17:31:56: #2 alternative fragment length(s) may be 3,144 bps INFO @ Mon, 03 Jun 2019 17:31:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.05_model.r INFO @ Mon, 03 Jun 2019 17:31:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:31:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:31:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:31:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.10_summits.bed INFO @ Mon, 03 Jun 2019 17:31:57: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (213 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:32:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:32:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.20_summits.bed INFO @ Mon, 03 Jun 2019 17:32:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650849/SRX4650849.05_summits.bed INFO @ Mon, 03 Jun 2019 17:32:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。