Job ID = 1294353 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:44:38 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 ) 2019-06-02T21:52:56 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 : 22,087,652 reads read : 44,175,304 reads written : 44,175,304 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: 00:47:34 22087652 reads; of these: 22087652 (100.00%) were paired; of these: 4698515 (21.27%) aligned concordantly 0 times 13384270 (60.60%) aligned concordantly exactly 1 time 4004867 (18.13%) aligned concordantly >1 times ---- 4698515 pairs aligned concordantly 0 times; of these: 985239 (20.97%) aligned discordantly 1 time ---- 3713276 pairs aligned 0 times concordantly or discordantly; of these: 7426552 mates make up the pairs; of these: 5573337 (75.05%) aligned 0 times 928445 (12.50%) aligned exactly 1 time 924770 (12.45%) aligned >1 times 87.38% overall alignment rate Time searching: 00:47:34 Overall time: 00:47:34 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 16 files... [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] 6142080 / 18280329 = 0.3360 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 08:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.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 08:00:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.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 08:00:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.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 08:00:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:31: 1000000 INFO @ Mon, 03 Jun 2019 08:00:34: 1000000 INFO @ Mon, 03 Jun 2019 08:00:34: 1000000 INFO @ Mon, 03 Jun 2019 08:00:39: 2000000 INFO @ Mon, 03 Jun 2019 08:00:43: 2000000 INFO @ Mon, 03 Jun 2019 08:00:46: 2000000 INFO @ Mon, 03 Jun 2019 08:00:47: 3000000 INFO @ Mon, 03 Jun 2019 08:00:51: 3000000 INFO @ Mon, 03 Jun 2019 08:00:54: 4000000 INFO @ Mon, 03 Jun 2019 08:00:57: 3000000 INFO @ Mon, 03 Jun 2019 08:01:00: 4000000 INFO @ Mon, 03 Jun 2019 08:01:02: 5000000 INFO @ Mon, 03 Jun 2019 08:01:08: 5000000 INFO @ Mon, 03 Jun 2019 08:01:09: 4000000 INFO @ Mon, 03 Jun 2019 08:01:09: 6000000 INFO @ Mon, 03 Jun 2019 08:01:17: 6000000 INFO @ Mon, 03 Jun 2019 08:01:17: 7000000 INFO @ Mon, 03 Jun 2019 08:01:21: 5000000 INFO @ Mon, 03 Jun 2019 08:01:25: 8000000 INFO @ Mon, 03 Jun 2019 08:01:25: 7000000 INFO @ Mon, 03 Jun 2019 08:01:32: 9000000 INFO @ Mon, 03 Jun 2019 08:01:33: 6000000 INFO @ Mon, 03 Jun 2019 08:01:34: 8000000 INFO @ Mon, 03 Jun 2019 08:01:40: 10000000 INFO @ Mon, 03 Jun 2019 08:01:42: 9000000 INFO @ Mon, 03 Jun 2019 08:01:45: 7000000 INFO @ Mon, 03 Jun 2019 08:01:47: 11000000 INFO @ Mon, 03 Jun 2019 08:01:51: 10000000 INFO @ Mon, 03 Jun 2019 08:01:55: 12000000 INFO @ Mon, 03 Jun 2019 08:01:57: 8000000 INFO @ Mon, 03 Jun 2019 08:01:59: 11000000 INFO @ Mon, 03 Jun 2019 08:02:02: 13000000 INFO @ Mon, 03 Jun 2019 08:02:08: 12000000 INFO @ Mon, 03 Jun 2019 08:02:08: 9000000 INFO @ Mon, 03 Jun 2019 08:02:10: 14000000 INFO @ Mon, 03 Jun 2019 08:02:16: 13000000 INFO @ Mon, 03 Jun 2019 08:02:17: 15000000 INFO @ Mon, 03 Jun 2019 08:02:21: 10000000 INFO @ Mon, 03 Jun 2019 08:02:26: 16000000 INFO @ Mon, 03 Jun 2019 08:02:26: 14000000 INFO @ Mon, 03 Jun 2019 08:02:32: 11000000 INFO @ Mon, 03 Jun 2019 08:02:34: 17000000 INFO @ Mon, 03 Jun 2019 08:02:36: 15000000 INFO @ Mon, 03 Jun 2019 08:02:42: 18000000 INFO @ Mon, 03 Jun 2019 08:02:44: 12000000 INFO @ Mon, 03 Jun 2019 08:02:44: 16000000 INFO @ Mon, 03 Jun 2019 08:02:49: 19000000 INFO @ Mon, 03 Jun 2019 08:02:53: 17000000 INFO @ Mon, 03 Jun 2019 08:02:56: 13000000 INFO @ Mon, 03 Jun 2019 08:02:57: 20000000 INFO @ Mon, 03 Jun 2019 08:03:01: 18000000 INFO @ Mon, 03 Jun 2019 08:03:04: 21000000 INFO @ Mon, 03 Jun 2019 08:03:07: 14000000 INFO @ Mon, 03 Jun 2019 08:03:09: 19000000 INFO @ Mon, 03 Jun 2019 08:03:12: 22000000 INFO @ Mon, 03 Jun 2019 08:03:17: 20000000 INFO @ Mon, 03 Jun 2019 08:03:18: 15000000 INFO @ Mon, 03 Jun 2019 08:03:19: 23000000 INFO @ Mon, 03 Jun 2019 08:03:26: 21000000 INFO @ Mon, 03 Jun 2019 08:03:26: 24000000 INFO @ Mon, 03 Jun 2019 08:03:30: 16000000 INFO @ Mon, 03 Jun 2019 08:03:34: 25000000 INFO @ Mon, 03 Jun 2019 08:03:34: 22000000 INFO @ Mon, 03 Jun 2019 08:03:41: 17000000 INFO @ Mon, 03 Jun 2019 08:03:41: 26000000 INFO @ Mon, 03 Jun 2019 08:03:42: 23000000 INFO @ Mon, 03 Jun 2019 08:03:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:03:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:03:43: #1 total tags in treatment: 11446549 INFO @ Mon, 03 Jun 2019 08:03:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:03:43: #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 08:03:44: #1 tags after filtering in treatment: 10239774 INFO @ Mon, 03 Jun 2019 08:03:44: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:03:44: #1 finished! INFO @ Mon, 03 Jun 2019 08:03:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:03:45: #2 number of paired peaks: 3865 INFO @ Mon, 03 Jun 2019 08:03:45: start model_add_line... INFO @ Mon, 03 Jun 2019 08:03:45: start X-correlation... INFO @ Mon, 03 Jun 2019 08:03:45: end of X-cor INFO @ Mon, 03 Jun 2019 08:03:45: #2 finished! INFO @ Mon, 03 Jun 2019 08:03:45: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 08:03:45: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 08:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.10_model.r INFO @ Mon, 03 Jun 2019 08:03:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:03:50: 24000000 INFO @ Mon, 03 Jun 2019 08:03:53: 18000000 INFO @ Mon, 03 Jun 2019 08:03:59: 25000000 INFO @ Mon, 03 Jun 2019 08:04:06: 19000000 INFO @ Mon, 03 Jun 2019 08:04:08: 26000000 INFO @ Mon, 03 Jun 2019 08:04:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:04:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:04:12: #1 total tags in treatment: 11446549 INFO @ Mon, 03 Jun 2019 08:04:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:04:12: #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 08:04:12: #1 tags after filtering in treatment: 10239774 INFO @ Mon, 03 Jun 2019 08:04:12: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:04:12: #1 finished! INFO @ Mon, 03 Jun 2019 08:04:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:04:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:04:13: #2 number of paired peaks: 3865 INFO @ Mon, 03 Jun 2019 08:04:13: start model_add_line... INFO @ Mon, 03 Jun 2019 08:04:13: start X-correlation... INFO @ Mon, 03 Jun 2019 08:04:13: end of X-cor INFO @ Mon, 03 Jun 2019 08:04:13: #2 finished! INFO @ Mon, 03 Jun 2019 08:04:13: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 08:04:13: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 08:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.05_model.r INFO @ Mon, 03 Jun 2019 08:04:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:04:20: 20000000 INFO @ Mon, 03 Jun 2019 08:04:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:04:34: 21000000 INFO @ Mon, 03 Jun 2019 08:04:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:04:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:04:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.10_summits.bed INFO @ Mon, 03 Jun 2019 08:04:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4700 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:04:48: 22000000 INFO @ Mon, 03 Jun 2019 08:04:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:05:02: 23000000 INFO @ Mon, 03 Jun 2019 08:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.05_summits.bed INFO @ Mon, 03 Jun 2019 08:05:07: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6432 records, 4 fields): 783 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:05:15: 24000000 INFO @ Mon, 03 Jun 2019 08:05:29: 25000000 INFO @ Mon, 03 Jun 2019 08:05:42: 26000000 INFO @ Mon, 03 Jun 2019 08:05:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:05:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:05:46: #1 total tags in treatment: 11446549 INFO @ Mon, 03 Jun 2019 08:05:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:05:46: #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 08:05:46: #1 tags after filtering in treatment: 10239774 INFO @ Mon, 03 Jun 2019 08:05:46: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:05:46: #1 finished! INFO @ Mon, 03 Jun 2019 08:05:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:05:48: #2 number of paired peaks: 3865 INFO @ Mon, 03 Jun 2019 08:05:48: start model_add_line... INFO @ Mon, 03 Jun 2019 08:05:48: start X-correlation... INFO @ Mon, 03 Jun 2019 08:05:48: end of X-cor INFO @ Mon, 03 Jun 2019 08:05:48: #2 finished! INFO @ Mon, 03 Jun 2019 08:05:48: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 08:05:48: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 08:05:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.20_model.r INFO @ Mon, 03 Jun 2019 08:05:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:05:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:06:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612518/SRX2612518.20_summits.bed INFO @ Mon, 03 Jun 2019 08:06:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3021 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。