Job ID = 1296968 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:40:37 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 : 40,740,942 reads read : 81,481,884 reads written : 81,481,884 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: 00:10:17 40740942 reads; of these: 40740942 (100.00%) were paired; of these: 39179080 (96.17%) aligned concordantly 0 times 1220238 (3.00%) aligned concordantly exactly 1 time 341624 (0.84%) aligned concordantly >1 times ---- 39179080 pairs aligned concordantly 0 times; of these: 7530 (0.02%) aligned discordantly 1 time ---- 39171550 pairs aligned 0 times concordantly or discordantly; of these: 78343100 mates make up the pairs; of these: 77464831 (98.88%) aligned 0 times 197312 (0.25%) aligned exactly 1 time 680957 (0.87%) aligned >1 times 4.93% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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] 73107 / 1566756 = 0.0467 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 17:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.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 17:08:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:08:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.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 17:08:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:08:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.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 17:08:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:08:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:08:42: 1000000 INFO @ Mon, 03 Jun 2019 17:08:42: 1000000 INFO @ Mon, 03 Jun 2019 17:08:43: 1000000 INFO @ Mon, 03 Jun 2019 17:08:50: 2000000 INFO @ Mon, 03 Jun 2019 17:08:50: 2000000 INFO @ Mon, 03 Jun 2019 17:08:52: 2000000 INFO @ Mon, 03 Jun 2019 17:08:57: 3000000 INFO @ Mon, 03 Jun 2019 17:08:58: 3000000 INFO @ Mon, 03 Jun 2019 17:09:00: 3000000 INFO @ Mon, 03 Jun 2019 17:09:03: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:09:03: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:09:03: #1 total tags in treatment: 1489020 INFO @ Mon, 03 Jun 2019 17:09:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:09:03: #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 17:09:03: #1 tags after filtering in treatment: 1441949 INFO @ Mon, 03 Jun 2019 17:09:03: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:09:03: #1 finished! INFO @ Mon, 03 Jun 2019 17:09:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:09:03: #2 number of paired peaks: 2491 INFO @ Mon, 03 Jun 2019 17:09:03: start model_add_line... INFO @ Mon, 03 Jun 2019 17:09:03: start X-correlation... INFO @ Mon, 03 Jun 2019 17:09:04: end of X-cor INFO @ Mon, 03 Jun 2019 17:09:04: #2 finished! INFO @ Mon, 03 Jun 2019 17:09:04: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 17:09:04: #2 alternative fragment length(s) may be 4,206,232,263 bps INFO @ Mon, 03 Jun 2019 17:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.05_model.r INFO @ Mon, 03 Jun 2019 17:09:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:09:04: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:09:04: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:09:04: #1 total tags in treatment: 1489020 INFO @ Mon, 03 Jun 2019 17:09:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:09:04: #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 17:09:04: #1 tags after filtering in treatment: 1441949 INFO @ Mon, 03 Jun 2019 17:09:04: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:09:04: #1 finished! INFO @ Mon, 03 Jun 2019 17:09:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:09:04: #2 number of paired peaks: 2491 INFO @ Mon, 03 Jun 2019 17:09:04: start model_add_line... INFO @ Mon, 03 Jun 2019 17:09:04: start X-correlation... INFO @ Mon, 03 Jun 2019 17:09:04: end of X-cor INFO @ Mon, 03 Jun 2019 17:09:04: #2 finished! INFO @ Mon, 03 Jun 2019 17:09:04: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 17:09:04: #2 alternative fragment length(s) may be 4,206,232,263 bps INFO @ Mon, 03 Jun 2019 17:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.10_model.r INFO @ Mon, 03 Jun 2019 17:09:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:09:07: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:09:07: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:09:07: #1 total tags in treatment: 1489020 INFO @ Mon, 03 Jun 2019 17:09:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:09:07: #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 17:09:07: #1 tags after filtering in treatment: 1441949 INFO @ Mon, 03 Jun 2019 17:09:07: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:09:07: #1 finished! INFO @ Mon, 03 Jun 2019 17:09:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:09:07: #2 number of paired peaks: 2491 INFO @ Mon, 03 Jun 2019 17:09:07: start model_add_line... INFO @ Mon, 03 Jun 2019 17:09:07: start X-correlation... INFO @ Mon, 03 Jun 2019 17:09:07: end of X-cor INFO @ Mon, 03 Jun 2019 17:09:07: #2 finished! INFO @ Mon, 03 Jun 2019 17:09:07: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 17:09:07: #2 alternative fragment length(s) may be 4,206,232,263 bps INFO @ Mon, 03 Jun 2019 17:09:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.20_model.r INFO @ Mon, 03 Jun 2019 17:09:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:09:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:09:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:09:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.05_summits.bed INFO @ Mon, 03 Jun 2019 17:09:11: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.10_summits.bed INFO @ Mon, 03 Jun 2019 17:09:11: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:09:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650822/SRX4650822.20_summits.bed INFO @ Mon, 03 Jun 2019 17:09:14: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。