Job ID = 1295158 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T03:20:41 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 ) 2019-06-03T03:30:41 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 : 47,715,000 reads read : 95,430,000 reads written : 95,430,000 spots read : 6,111,003 reads read : 12,222,006 reads written : 12,222,006 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: 01:56:26 53826003 reads; of these: 53826003 (100.00%) were paired; of these: 10874345 (20.20%) aligned concordantly 0 times 30115001 (55.95%) aligned concordantly exactly 1 time 12836657 (23.85%) aligned concordantly >1 times ---- 10874345 pairs aligned concordantly 0 times; of these: 1181859 (10.87%) aligned discordantly 1 time ---- 9692486 pairs aligned 0 times concordantly or discordantly; of these: 19384972 mates make up the pairs; of these: 14768816 (76.19%) aligned 0 times 2257180 (11.64%) aligned exactly 1 time 2358976 (12.17%) aligned >1 times 86.28% overall alignment rate Time searching: 01:56:26 Overall time: 01:56:26 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 32 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] 36327280 / 43689210 = 0.8315 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 15:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.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 15:05:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:05:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.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 15:05:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:05:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.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 15:05:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:05:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:05:34: 1000000 INFO @ Mon, 03 Jun 2019 15:05:34: 1000000 INFO @ Mon, 03 Jun 2019 15:05:36: 1000000 INFO @ Mon, 03 Jun 2019 15:05:39: 2000000 INFO @ Mon, 03 Jun 2019 15:05:41: 2000000 INFO @ Mon, 03 Jun 2019 15:05:44: 2000000 INFO @ Mon, 03 Jun 2019 15:05:45: 3000000 INFO @ Mon, 03 Jun 2019 15:05:47: 3000000 INFO @ Mon, 03 Jun 2019 15:05:51: 4000000 INFO @ Mon, 03 Jun 2019 15:05:52: 3000000 INFO @ Mon, 03 Jun 2019 15:05:53: 4000000 INFO @ Mon, 03 Jun 2019 15:05:56: 5000000 INFO @ Mon, 03 Jun 2019 15:05:59: 5000000 INFO @ Mon, 03 Jun 2019 15:05:59: 4000000 INFO @ Mon, 03 Jun 2019 15:06:02: 6000000 INFO @ Mon, 03 Jun 2019 15:06:05: 6000000 INFO @ Mon, 03 Jun 2019 15:06:07: 5000000 INFO @ Mon, 03 Jun 2019 15:06:08: 7000000 INFO @ Mon, 03 Jun 2019 15:06:11: 7000000 INFO @ Mon, 03 Jun 2019 15:06:13: 8000000 INFO @ Mon, 03 Jun 2019 15:06:15: 6000000 INFO @ Mon, 03 Jun 2019 15:06:18: 8000000 INFO @ Mon, 03 Jun 2019 15:06:20: 9000000 INFO @ Mon, 03 Jun 2019 15:06:22: 7000000 INFO @ Mon, 03 Jun 2019 15:06:24: 9000000 INFO @ Mon, 03 Jun 2019 15:06:26: 10000000 INFO @ Mon, 03 Jun 2019 15:06:30: 8000000 INFO @ Mon, 03 Jun 2019 15:06:30: 10000000 INFO @ Mon, 03 Jun 2019 15:06:31: 11000000 INFO @ Mon, 03 Jun 2019 15:06:37: 11000000 INFO @ Mon, 03 Jun 2019 15:06:37: 12000000 INFO @ Mon, 03 Jun 2019 15:06:38: 9000000 INFO @ Mon, 03 Jun 2019 15:06:43: 12000000 INFO @ Mon, 03 Jun 2019 15:06:43: 13000000 INFO @ Mon, 03 Jun 2019 15:06:45: 10000000 INFO @ Mon, 03 Jun 2019 15:06:49: 14000000 INFO @ Mon, 03 Jun 2019 15:06:49: 13000000 INFO @ Mon, 03 Jun 2019 15:06:53: 11000000 INFO @ Mon, 03 Jun 2019 15:06:55: 15000000 INFO @ Mon, 03 Jun 2019 15:06:56: 14000000 INFO @ Mon, 03 Jun 2019 15:07:01: 12000000 INFO @ Mon, 03 Jun 2019 15:07:01: 16000000 INFO @ Mon, 03 Jun 2019 15:07:02: 15000000 INFO @ Mon, 03 Jun 2019 15:07:07: 17000000 INFO @ Mon, 03 Jun 2019 15:07:08: 13000000 INFO @ Mon, 03 Jun 2019 15:07:08: 16000000 INFO @ Mon, 03 Jun 2019 15:07:12: 18000000 INFO @ Mon, 03 Jun 2019 15:07:15: 17000000 INFO @ Mon, 03 Jun 2019 15:07:16: 14000000 INFO @ Mon, 03 Jun 2019 15:07:18: 19000000 INFO @ Mon, 03 Jun 2019 15:07:21: 18000000 INFO @ Mon, 03 Jun 2019 15:07:24: 15000000 INFO @ Mon, 03 Jun 2019 15:07:24: 20000000 INFO @ Mon, 03 Jun 2019 15:07:25: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 15:07:25: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 15:07:25: #1 total tags in treatment: 7576440 INFO @ Mon, 03 Jun 2019 15:07:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:07:25: #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 15:07:25: #1 tags after filtering in treatment: 5614164 INFO @ Mon, 03 Jun 2019 15:07:25: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 15:07:25: #1 finished! INFO @ Mon, 03 Jun 2019 15:07:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:07:27: #2 number of paired peaks: 7396 INFO @ Mon, 03 Jun 2019 15:07:27: start model_add_line... INFO @ Mon, 03 Jun 2019 15:07:27: start X-correlation... INFO @ Mon, 03 Jun 2019 15:07:27: end of X-cor INFO @ Mon, 03 Jun 2019 15:07:27: #2 finished! INFO @ Mon, 03 Jun 2019 15:07:27: #2 predicted fragment length is 88 bps INFO @ Mon, 03 Jun 2019 15:07:27: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 03 Jun 2019 15:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.05_model.r INFO @ Mon, 03 Jun 2019 15:07:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:07:27: 19000000 INFO @ Mon, 03 Jun 2019 15:07:31: 16000000 INFO @ Mon, 03 Jun 2019 15:07:33: 20000000 INFO @ Mon, 03 Jun 2019 15:07:35: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 15:07:35: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 15:07:35: #1 total tags in treatment: 7576440 INFO @ Mon, 03 Jun 2019 15:07:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:07:35: #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 15:07:35: #1 tags after filtering in treatment: 5614164 INFO @ Mon, 03 Jun 2019 15:07:35: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 15:07:35: #1 finished! INFO @ Mon, 03 Jun 2019 15:07:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:07:36: #2 number of paired peaks: 7396 INFO @ Mon, 03 Jun 2019 15:07:36: start model_add_line... INFO @ Mon, 03 Jun 2019 15:07:36: start X-correlation... INFO @ Mon, 03 Jun 2019 15:07:36: end of X-cor INFO @ Mon, 03 Jun 2019 15:07:36: #2 finished! INFO @ Mon, 03 Jun 2019 15:07:36: #2 predicted fragment length is 88 bps INFO @ Mon, 03 Jun 2019 15:07:36: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 03 Jun 2019 15:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.10_model.r INFO @ Mon, 03 Jun 2019 15:07:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:07:39: 17000000 INFO @ Mon, 03 Jun 2019 15:07:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:07:46: 18000000 INFO @ Mon, 03 Jun 2019 15:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:07:54: 19000000 INFO @ Mon, 03 Jun 2019 15:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:07:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.05_summits.bed INFO @ Mon, 03 Jun 2019 15:07:54: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11980 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:08:01: 20000000 INFO @ Mon, 03 Jun 2019 15:08:03: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 15:08:03: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 15:08:03: #1 total tags in treatment: 7576440 INFO @ Mon, 03 Jun 2019 15:08:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:08:03: #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 15:08:03: #1 tags after filtering in treatment: 5614164 INFO @ Mon, 03 Jun 2019 15:08:03: #1 Redundant rate of treatment: 0.26 INFO @ Mon, 03 Jun 2019 15:08:03: #1 finished! INFO @ Mon, 03 Jun 2019 15:08:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.10_summits.bed INFO @ Mon, 03 Jun 2019 15:08:03: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8220 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:08:04: #2 number of paired peaks: 7396 INFO @ Mon, 03 Jun 2019 15:08:04: start model_add_line... INFO @ Mon, 03 Jun 2019 15:08:04: start X-correlation... INFO @ Mon, 03 Jun 2019 15:08:04: end of X-cor INFO @ Mon, 03 Jun 2019 15:08:04: #2 finished! INFO @ Mon, 03 Jun 2019 15:08:04: #2 predicted fragment length is 88 bps INFO @ Mon, 03 Jun 2019 15:08:04: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 03 Jun 2019 15:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.20_model.r INFO @ Mon, 03 Jun 2019 15:08:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:08:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287351/SRX3287351.20_summits.bed INFO @ Mon, 03 Jun 2019 15:08:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4254 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。