Job ID = 1295160 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 ) 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 ) 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 : 33,798,035 reads read : 67,596,070 reads written : 67,596,070 spots read : 2,563,826 reads read : 5,127,652 reads written : 5,127,652 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: 01:44:22 36361861 reads; of these: 36361861 (100.00%) were paired; of these: 6657507 (18.31%) aligned concordantly 0 times 17874801 (49.16%) aligned concordantly exactly 1 time 11829553 (32.53%) aligned concordantly >1 times ---- 6657507 pairs aligned concordantly 0 times; of these: 498251 (7.48%) aligned discordantly 1 time ---- 6159256 pairs aligned 0 times concordantly or discordantly; of these: 12318512 mates make up the pairs; of these: 8845041 (71.80%) aligned 0 times 1631321 (13.24%) aligned exactly 1 time 1842150 (14.95%) aligned >1 times 87.84% overall alignment rate Time searching: 01:44:22 Overall time: 01:44:22 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 20 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] 25448363 / 29949752 = 0.8497 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 14:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.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 14:34:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:34:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.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 14:34:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:34:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.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 14:34:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:34:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:34:32: 1000000 INFO @ Mon, 03 Jun 2019 14:34:32: 1000000 INFO @ Mon, 03 Jun 2019 14:34:32: 1000000 INFO @ Mon, 03 Jun 2019 14:34:41: 2000000 INFO @ Mon, 03 Jun 2019 14:34:41: 2000000 INFO @ Mon, 03 Jun 2019 14:34:42: 2000000 INFO @ Mon, 03 Jun 2019 14:34:50: 3000000 INFO @ Mon, 03 Jun 2019 14:34:50: 3000000 INFO @ Mon, 03 Jun 2019 14:34:52: 3000000 INFO @ Mon, 03 Jun 2019 14:34:59: 4000000 INFO @ Mon, 03 Jun 2019 14:34:59: 4000000 INFO @ Mon, 03 Jun 2019 14:35:03: 4000000 INFO @ Mon, 03 Jun 2019 14:35:07: 5000000 INFO @ Mon, 03 Jun 2019 14:35:08: 5000000 INFO @ Mon, 03 Jun 2019 14:35:13: 5000000 INFO @ Mon, 03 Jun 2019 14:35:15: 6000000 INFO @ Mon, 03 Jun 2019 14:35:18: 6000000 INFO @ Mon, 03 Jun 2019 14:35:23: 6000000 INFO @ Mon, 03 Jun 2019 14:35:24: 7000000 INFO @ Mon, 03 Jun 2019 14:35:27: 7000000 INFO @ Mon, 03 Jun 2019 14:35:33: 8000000 INFO @ Mon, 03 Jun 2019 14:35:34: 7000000 INFO @ Mon, 03 Jun 2019 14:35:36: 8000000 INFO @ Mon, 03 Jun 2019 14:35:42: 9000000 INFO @ Mon, 03 Jun 2019 14:35:45: 8000000 INFO @ Mon, 03 Jun 2019 14:35:46: 9000000 INFO @ Mon, 03 Jun 2019 14:35:53: 10000000 INFO @ Mon, 03 Jun 2019 14:35:55: 9000000 INFO @ Mon, 03 Jun 2019 14:35:55: 10000000 INFO @ Mon, 03 Jun 2019 14:36:03: 11000000 INFO @ Mon, 03 Jun 2019 14:36:05: 10000000 INFO @ Mon, 03 Jun 2019 14:36:06: 11000000 INFO @ Mon, 03 Jun 2019 14:36:13: 12000000 INFO @ Mon, 03 Jun 2019 14:36:15: 12000000 INFO @ Mon, 03 Jun 2019 14:36:16: 11000000 INFO @ Mon, 03 Jun 2019 14:36:21: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 14:36:21: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 14:36:21: #1 total tags in treatment: 4636640 INFO @ Mon, 03 Jun 2019 14:36:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:36:21: #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 14:36:22: #1 tags after filtering in treatment: 3548871 INFO @ Mon, 03 Jun 2019 14:36:22: #1 Redundant rate of treatment: 0.23 INFO @ Mon, 03 Jun 2019 14:36:22: #1 finished! INFO @ Mon, 03 Jun 2019 14:36:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:36:22: #2 number of paired peaks: 7877 INFO @ Mon, 03 Jun 2019 14:36:22: start model_add_line... INFO @ Mon, 03 Jun 2019 14:36:23: start X-correlation... INFO @ Mon, 03 Jun 2019 14:36:23: end of X-cor INFO @ Mon, 03 Jun 2019 14:36:23: #2 finished! INFO @ Mon, 03 Jun 2019 14:36:23: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 14:36:23: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 14:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.20_model.r INFO @ Mon, 03 Jun 2019 14:36:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:36:24: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 14:36:24: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 14:36:24: #1 total tags in treatment: 4636640 INFO @ Mon, 03 Jun 2019 14:36:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:36:24: #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 14:36:24: #1 tags after filtering in treatment: 3548871 INFO @ Mon, 03 Jun 2019 14:36:24: #1 Redundant rate of treatment: 0.23 INFO @ Mon, 03 Jun 2019 14:36:24: #1 finished! INFO @ Mon, 03 Jun 2019 14:36:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:36:25: #2 number of paired peaks: 7877 INFO @ Mon, 03 Jun 2019 14:36:25: start model_add_line... INFO @ Mon, 03 Jun 2019 14:36:25: start X-correlation... INFO @ Mon, 03 Jun 2019 14:36:25: end of X-cor INFO @ Mon, 03 Jun 2019 14:36:25: #2 finished! INFO @ Mon, 03 Jun 2019 14:36:25: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 14:36:25: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 14:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.05_model.r INFO @ Mon, 03 Jun 2019 14:36:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:36:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:36:26: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 14:36:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:36:35: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 14:36:35: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 14:36:35: #1 total tags in treatment: 4636640 INFO @ Mon, 03 Jun 2019 14:36:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:36:35: #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 14:36:35: #1 tags after filtering in treatment: 3548871 INFO @ Mon, 03 Jun 2019 14:36:35: #1 Redundant rate of treatment: 0.23 INFO @ Mon, 03 Jun 2019 14:36:35: #1 finished! INFO @ Mon, 03 Jun 2019 14:36:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:36:36: #2 number of paired peaks: 7877 INFO @ Mon, 03 Jun 2019 14:36:36: start model_add_line... INFO @ Mon, 03 Jun 2019 14:36:36: start X-correlation... INFO @ Mon, 03 Jun 2019 14:36:36: end of X-cor INFO @ Mon, 03 Jun 2019 14:36:36: #2 finished! INFO @ Mon, 03 Jun 2019 14:36:36: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 14:36:36: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 14:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.10_model.r INFO @ Mon, 03 Jun 2019 14:36:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:36:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.20_summits.bed INFO @ Mon, 03 Jun 2019 14:36:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2702 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.05_summits.bed INFO @ Mon, 03 Jun 2019 14:36:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8160 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 14:36:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287353/SRX3287353.10_summits.bed INFO @ Mon, 03 Jun 2019 14:36:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5495 records, 4 fields): 8 millis CompletedMACS2peakCalling