Job ID = 1294340 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:36:58 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 ) 2019-06-02T21:36:58 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 : 17,059,843 reads read : 34,119,686 reads written : 34,119,686 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: 00:51:24 17059843 reads; of these: 17059843 (100.00%) were paired; of these: 530340 (3.11%) aligned concordantly 0 times 12889125 (75.55%) aligned concordantly exactly 1 time 3640378 (21.34%) aligned concordantly >1 times ---- 530340 pairs aligned concordantly 0 times; of these: 9959 (1.88%) aligned discordantly 1 time ---- 520381 pairs aligned 0 times concordantly or discordantly; of these: 1040762 mates make up the pairs; of these: 793154 (76.21%) aligned 0 times 172378 (16.56%) aligned exactly 1 time 75230 (7.23%) aligned >1 times 97.68% overall alignment rate Time searching: 00:51:24 Overall time: 00:51:24 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] 2253046 / 16528880 = 0.1363 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 07:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.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 07:57:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.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 07:57:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.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 07:57:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:41: 1000000 INFO @ Mon, 03 Jun 2019 07:57:42: 1000000 INFO @ Mon, 03 Jun 2019 07:57:42: 1000000 INFO @ Mon, 03 Jun 2019 07:57:53: 2000000 INFO @ Mon, 03 Jun 2019 07:57:55: 2000000 INFO @ Mon, 03 Jun 2019 07:57:56: 2000000 INFO @ Mon, 03 Jun 2019 07:58:04: 3000000 INFO @ Mon, 03 Jun 2019 07:58:08: 3000000 INFO @ Mon, 03 Jun 2019 07:58:08: 3000000 INFO @ Mon, 03 Jun 2019 07:58:15: 4000000 INFO @ Mon, 03 Jun 2019 07:58:21: 4000000 INFO @ Mon, 03 Jun 2019 07:58:21: 4000000 INFO @ Mon, 03 Jun 2019 07:58:27: 5000000 INFO @ Mon, 03 Jun 2019 07:58:34: 5000000 INFO @ Mon, 03 Jun 2019 07:58:34: 5000000 INFO @ Mon, 03 Jun 2019 07:58:40: 6000000 INFO @ Mon, 03 Jun 2019 07:58:46: 6000000 INFO @ Mon, 03 Jun 2019 07:58:47: 6000000 INFO @ Mon, 03 Jun 2019 07:58:52: 7000000 INFO @ Mon, 03 Jun 2019 07:58:57: 7000000 INFO @ Mon, 03 Jun 2019 07:59:00: 7000000 INFO @ Mon, 03 Jun 2019 07:59:05: 8000000 INFO @ Mon, 03 Jun 2019 07:59:09: 8000000 INFO @ Mon, 03 Jun 2019 07:59:12: 8000000 INFO @ Mon, 03 Jun 2019 07:59:17: 9000000 INFO @ Mon, 03 Jun 2019 07:59:20: 9000000 INFO @ Mon, 03 Jun 2019 07:59:25: 9000000 INFO @ Mon, 03 Jun 2019 07:59:29: 10000000 INFO @ Mon, 03 Jun 2019 07:59:31: 10000000 INFO @ Mon, 03 Jun 2019 07:59:37: 10000000 INFO @ Mon, 03 Jun 2019 07:59:42: 11000000 INFO @ Mon, 03 Jun 2019 07:59:43: 11000000 INFO @ Mon, 03 Jun 2019 07:59:50: 11000000 INFO @ Mon, 03 Jun 2019 07:59:54: 12000000 INFO @ Mon, 03 Jun 2019 07:59:55: 12000000 INFO @ Mon, 03 Jun 2019 08:00:03: 12000000 INFO @ Mon, 03 Jun 2019 08:00:05: 13000000 INFO @ Mon, 03 Jun 2019 08:00:08: 13000000 INFO @ Mon, 03 Jun 2019 08:00:15: 13000000 INFO @ Mon, 03 Jun 2019 08:00:17: 14000000 INFO @ Mon, 03 Jun 2019 08:00:20: 14000000 INFO @ Mon, 03 Jun 2019 08:00:27: 14000000 INFO @ Mon, 03 Jun 2019 08:00:28: 15000000 INFO @ Mon, 03 Jun 2019 08:00:33: 15000000 INFO @ Mon, 03 Jun 2019 08:00:40: 16000000 INFO @ Mon, 03 Jun 2019 08:00:40: 15000000 INFO @ Mon, 03 Jun 2019 08:00:46: 16000000 INFO @ Mon, 03 Jun 2019 08:00:51: 17000000 INFO @ Mon, 03 Jun 2019 08:00:53: 16000000 INFO @ Mon, 03 Jun 2019 08:00:59: 17000000 INFO @ Mon, 03 Jun 2019 08:01:02: 18000000 INFO @ Mon, 03 Jun 2019 08:01:04: 17000000 INFO @ Mon, 03 Jun 2019 08:01:12: 18000000 INFO @ Mon, 03 Jun 2019 08:01:14: 19000000 INFO @ Mon, 03 Jun 2019 08:01:15: 18000000 INFO @ Mon, 03 Jun 2019 08:01:25: 19000000 INFO @ Mon, 03 Jun 2019 08:01:26: 20000000 INFO @ Mon, 03 Jun 2019 08:01:26: 19000000 INFO @ Mon, 03 Jun 2019 08:01:38: 21000000 INFO @ Mon, 03 Jun 2019 08:01:39: 20000000 INFO @ Mon, 03 Jun 2019 08:01:40: 20000000 INFO @ Mon, 03 Jun 2019 08:01:51: 22000000 INFO @ Mon, 03 Jun 2019 08:01:52: 21000000 INFO @ Mon, 03 Jun 2019 08:01:53: 21000000 INFO @ Mon, 03 Jun 2019 08:02:02: 23000000 INFO @ Mon, 03 Jun 2019 08:02:03: 22000000 INFO @ Mon, 03 Jun 2019 08:02:06: 22000000 INFO @ Mon, 03 Jun 2019 08:02:14: 24000000 INFO @ Mon, 03 Jun 2019 08:02:15: 23000000 INFO @ Mon, 03 Jun 2019 08:02:20: 23000000 INFO @ Mon, 03 Jun 2019 08:02:25: 25000000 INFO @ Mon, 03 Jun 2019 08:02:27: 24000000 INFO @ Mon, 03 Jun 2019 08:02:33: 24000000 INFO @ Mon, 03 Jun 2019 08:02:36: 26000000 INFO @ Mon, 03 Jun 2019 08:02:38: 25000000 INFO @ Mon, 03 Jun 2019 08:02:45: 25000000 INFO @ Mon, 03 Jun 2019 08:02:47: 27000000 INFO @ Mon, 03 Jun 2019 08:02:49: 26000000 INFO @ Mon, 03 Jun 2019 08:02:58: 26000000 INFO @ Mon, 03 Jun 2019 08:02:58: 28000000 INFO @ Mon, 03 Jun 2019 08:03:01: 27000000 INFO @ Mon, 03 Jun 2019 08:03:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:03:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:03:08: #1 total tags in treatment: 14276858 INFO @ Mon, 03 Jun 2019 08:03:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:03:08: #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 08:03:08: #1 tags after filtering in treatment: 12714276 INFO @ Mon, 03 Jun 2019 08:03:08: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:03:08: #1 finished! INFO @ Mon, 03 Jun 2019 08:03:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:03:10: #2 number of paired peaks: 887 WARNING @ Mon, 03 Jun 2019 08:03:10: Fewer paired peaks (887) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 887 pairs to build model! INFO @ Mon, 03 Jun 2019 08:03:10: start model_add_line... INFO @ Mon, 03 Jun 2019 08:03:10: start X-correlation... INFO @ Mon, 03 Jun 2019 08:03:10: end of X-cor INFO @ Mon, 03 Jun 2019 08:03:10: #2 finished! INFO @ Mon, 03 Jun 2019 08:03:10: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 08:03:10: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 08:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.05_model.r INFO @ Mon, 03 Jun 2019 08:03:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:03:11: 27000000 INFO @ Mon, 03 Jun 2019 08:03:12: 28000000 INFO @ Mon, 03 Jun 2019 08:03:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:03:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:03:21: #1 total tags in treatment: 14276858 INFO @ Mon, 03 Jun 2019 08:03:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:03:21: #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 08:03:21: #1 tags after filtering in treatment: 12714276 INFO @ Mon, 03 Jun 2019 08:03:21: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:03:21: #1 finished! INFO @ Mon, 03 Jun 2019 08:03:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:03:23: #2 number of paired peaks: 887 WARNING @ Mon, 03 Jun 2019 08:03:23: Fewer paired peaks (887) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 887 pairs to build model! INFO @ Mon, 03 Jun 2019 08:03:23: start model_add_line... INFO @ Mon, 03 Jun 2019 08:03:23: start X-correlation... INFO @ Mon, 03 Jun 2019 08:03:23: end of X-cor INFO @ Mon, 03 Jun 2019 08:03:23: #2 finished! INFO @ Mon, 03 Jun 2019 08:03:23: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 08:03:23: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 08:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.20_model.r INFO @ Mon, 03 Jun 2019 08:03:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:03:23: 28000000 INFO @ Mon, 03 Jun 2019 08:03:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:03:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:03:34: #1 total tags in treatment: 14276858 INFO @ Mon, 03 Jun 2019 08:03:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:03:34: #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 08:03:35: #1 tags after filtering in treatment: 12714276 INFO @ Mon, 03 Jun 2019 08:03:35: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:03:35: #1 finished! INFO @ Mon, 03 Jun 2019 08:03:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:03:36: #2 number of paired peaks: 887 WARNING @ Mon, 03 Jun 2019 08:03:36: Fewer paired peaks (887) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 887 pairs to build model! INFO @ Mon, 03 Jun 2019 08:03:36: start model_add_line... INFO @ Mon, 03 Jun 2019 08:03:37: start X-correlation... INFO @ Mon, 03 Jun 2019 08:03:37: end of X-cor INFO @ Mon, 03 Jun 2019 08:03:37: #2 finished! INFO @ Mon, 03 Jun 2019 08:03:37: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 08:03:37: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 08:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.10_model.r INFO @ Mon, 03 Jun 2019 08:03:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:03:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:04:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.05_summits.bed INFO @ Mon, 03 Jun 2019 08:04:27: Done! INFO @ Mon, 03 Jun 2019 08:04:27: #3 Call peaks for each chromosome... pass1 - making usageList (14 chroms): 14 millis pass2 - checking and writing primary data (36192 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:04:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:04:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:04:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.20_summits.bed INFO @ Mon, 03 Jun 2019 08:04:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5554 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:04:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:04:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:04:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252230/SRX252230.10_summits.bed INFO @ Mon, 03 Jun 2019 08:04:56: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (18236 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。