Job ID = 1294173 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T20:16:30 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 ) 2019-06-02T20:16:30 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 ) 2019-06-02T20:16:30 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 ) 2019-06-02T20:16:30 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 ) 2019-06-02T20:19:40 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 : 51,341,121 reads read : 102,682,242 reads written : 102,682,242 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: 00:46:45 51341121 reads; of these: 51341121 (100.00%) were paired; of these: 18990749 (36.99%) aligned concordantly 0 times 28958352 (56.40%) aligned concordantly exactly 1 time 3392020 (6.61%) aligned concordantly >1 times ---- 18990749 pairs aligned concordantly 0 times; of these: 740631 (3.90%) aligned discordantly 1 time ---- 18250118 pairs aligned 0 times concordantly or discordantly; of these: 36500236 mates make up the pairs; of these: 34817927 (95.39%) aligned 0 times 1327166 (3.64%) aligned exactly 1 time 355143 (0.97%) aligned >1 times 66.09% overall alignment rate Time searching: 00:46:45 Overall time: 00:46:45 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 28 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] 16954391 / 32959918 = 0.5144 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 06:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.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 06:27:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:27:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.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 06:27:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:27:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.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 06:27:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:27:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:27:56: 1000000 INFO @ Mon, 03 Jun 2019 06:27:56: 1000000 INFO @ Mon, 03 Jun 2019 06:27:56: 1000000 INFO @ Mon, 03 Jun 2019 06:28:03: 2000000 INFO @ Mon, 03 Jun 2019 06:28:03: 2000000 INFO @ Mon, 03 Jun 2019 06:28:04: 2000000 INFO @ Mon, 03 Jun 2019 06:28:09: 3000000 INFO @ Mon, 03 Jun 2019 06:28:10: 3000000 INFO @ Mon, 03 Jun 2019 06:28:12: 3000000 INFO @ Mon, 03 Jun 2019 06:28:16: 4000000 INFO @ Mon, 03 Jun 2019 06:28:18: 4000000 INFO @ Mon, 03 Jun 2019 06:28:20: 4000000 INFO @ Mon, 03 Jun 2019 06:28:23: 5000000 INFO @ Mon, 03 Jun 2019 06:28:26: 5000000 INFO @ Mon, 03 Jun 2019 06:28:28: 5000000 INFO @ Mon, 03 Jun 2019 06:28:31: 6000000 INFO @ Mon, 03 Jun 2019 06:28:33: 6000000 INFO @ Mon, 03 Jun 2019 06:28:35: 6000000 INFO @ Mon, 03 Jun 2019 06:28:38: 7000000 INFO @ Mon, 03 Jun 2019 06:28:40: 7000000 INFO @ Mon, 03 Jun 2019 06:28:42: 7000000 INFO @ Mon, 03 Jun 2019 06:28:45: 8000000 INFO @ Mon, 03 Jun 2019 06:28:47: 8000000 INFO @ Mon, 03 Jun 2019 06:28:48: 8000000 INFO @ Mon, 03 Jun 2019 06:28:52: 9000000 INFO @ Mon, 03 Jun 2019 06:28:54: 9000000 INFO @ Mon, 03 Jun 2019 06:28:55: 9000000 INFO @ Mon, 03 Jun 2019 06:28:59: 10000000 INFO @ Mon, 03 Jun 2019 06:29:01: 10000000 INFO @ Mon, 03 Jun 2019 06:29:02: 10000000 INFO @ Mon, 03 Jun 2019 06:29:05: 11000000 INFO @ Mon, 03 Jun 2019 06:29:08: 11000000 INFO @ Mon, 03 Jun 2019 06:29:09: 11000000 INFO @ Mon, 03 Jun 2019 06:29:11: 12000000 INFO @ Mon, 03 Jun 2019 06:29:15: 12000000 INFO @ Mon, 03 Jun 2019 06:29:16: 12000000 INFO @ Mon, 03 Jun 2019 06:29:18: 13000000 INFO @ Mon, 03 Jun 2019 06:29:22: 13000000 INFO @ Mon, 03 Jun 2019 06:29:22: 13000000 INFO @ Mon, 03 Jun 2019 06:29:24: 14000000 INFO @ Mon, 03 Jun 2019 06:29:29: 14000000 INFO @ Mon, 03 Jun 2019 06:29:29: 14000000 INFO @ Mon, 03 Jun 2019 06:29:31: 15000000 INFO @ Mon, 03 Jun 2019 06:29:36: 15000000 INFO @ Mon, 03 Jun 2019 06:29:36: 15000000 INFO @ Mon, 03 Jun 2019 06:29:37: 16000000 INFO @ Mon, 03 Jun 2019 06:29:43: 16000000 INFO @ Mon, 03 Jun 2019 06:29:44: 16000000 INFO @ Mon, 03 Jun 2019 06:29:44: 17000000 INFO @ Mon, 03 Jun 2019 06:29:50: 17000000 INFO @ Mon, 03 Jun 2019 06:29:51: 17000000 INFO @ Mon, 03 Jun 2019 06:29:52: 18000000 INFO @ Mon, 03 Jun 2019 06:29:57: 18000000 INFO @ Mon, 03 Jun 2019 06:29:58: 19000000 INFO @ Mon, 03 Jun 2019 06:29:58: 18000000 INFO @ Mon, 03 Jun 2019 06:30:03: 19000000 INFO @ Mon, 03 Jun 2019 06:30:04: 20000000 INFO @ Mon, 03 Jun 2019 06:30:05: 19000000 INFO @ Mon, 03 Jun 2019 06:30:10: 20000000 INFO @ Mon, 03 Jun 2019 06:30:11: 21000000 INFO @ Mon, 03 Jun 2019 06:30:12: 20000000 INFO @ Mon, 03 Jun 2019 06:30:17: 21000000 INFO @ Mon, 03 Jun 2019 06:30:17: 22000000 INFO @ Mon, 03 Jun 2019 06:30:18: 21000000 INFO @ Mon, 03 Jun 2019 06:30:23: 22000000 INFO @ Mon, 03 Jun 2019 06:30:24: 23000000 INFO @ Mon, 03 Jun 2019 06:30:25: 22000000 INFO @ Mon, 03 Jun 2019 06:30:30: 24000000 INFO @ Mon, 03 Jun 2019 06:30:32: 23000000 INFO @ Mon, 03 Jun 2019 06:30:32: 23000000 INFO @ Mon, 03 Jun 2019 06:30:37: 25000000 INFO @ Mon, 03 Jun 2019 06:30:39: 24000000 INFO @ Mon, 03 Jun 2019 06:30:40: 24000000 INFO @ Mon, 03 Jun 2019 06:30:43: 26000000 INFO @ Mon, 03 Jun 2019 06:30:46: 25000000 INFO @ Mon, 03 Jun 2019 06:30:47: 25000000 INFO @ Mon, 03 Jun 2019 06:30:50: 27000000 INFO @ Mon, 03 Jun 2019 06:30:52: 26000000 INFO @ Mon, 03 Jun 2019 06:30:54: 26000000 INFO @ Mon, 03 Jun 2019 06:30:56: 28000000 INFO @ Mon, 03 Jun 2019 06:31:00: 27000000 INFO @ Mon, 03 Jun 2019 06:31:01: 27000000 INFO @ Mon, 03 Jun 2019 06:31:03: 29000000 INFO @ Mon, 03 Jun 2019 06:31:09: 28000000 INFO @ Mon, 03 Jun 2019 06:31:09: 28000000 INFO @ Mon, 03 Jun 2019 06:31:11: 30000000 INFO @ Mon, 03 Jun 2019 06:31:17: 29000000 INFO @ Mon, 03 Jun 2019 06:31:17: 29000000 INFO @ Mon, 03 Jun 2019 06:31:17: 31000000 INFO @ Mon, 03 Jun 2019 06:31:24: 32000000 INFO @ Mon, 03 Jun 2019 06:31:24: 30000000 INFO @ Mon, 03 Jun 2019 06:31:25: 30000000 INFO @ Mon, 03 Jun 2019 06:31:31: 33000000 INFO @ Mon, 03 Jun 2019 06:31:32: 31000000 INFO @ Mon, 03 Jun 2019 06:31:33: 31000000 INFO @ Mon, 03 Jun 2019 06:31:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:31:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:31:37: #1 total tags in treatment: 15726030 INFO @ Mon, 03 Jun 2019 06:31:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:31:37: #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 06:31:38: #1 tags after filtering in treatment: 13263095 INFO @ Mon, 03 Jun 2019 06:31:38: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 03 Jun 2019 06:31:38: #1 finished! INFO @ Mon, 03 Jun 2019 06:31:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:31:39: 32000000 INFO @ Mon, 03 Jun 2019 06:31:40: #2 number of paired peaks: 7630 INFO @ Mon, 03 Jun 2019 06:31:40: start model_add_line... INFO @ Mon, 03 Jun 2019 06:31:40: start X-correlation... INFO @ Mon, 03 Jun 2019 06:31:40: end of X-cor INFO @ Mon, 03 Jun 2019 06:31:40: #2 finished! INFO @ Mon, 03 Jun 2019 06:31:40: #2 predicted fragment length is 164 bps INFO @ Mon, 03 Jun 2019 06:31:40: #2 alternative fragment length(s) may be 2,164 bps INFO @ Mon, 03 Jun 2019 06:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.05_model.r INFO @ Mon, 03 Jun 2019 06:31:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:31:41: 32000000 INFO @ Mon, 03 Jun 2019 06:31:47: 33000000 INFO @ Mon, 03 Jun 2019 06:31:48: 33000000 INFO @ Mon, 03 Jun 2019 06:31:55: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:31:55: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:31:55: #1 total tags in treatment: 15726030 INFO @ Mon, 03 Jun 2019 06:31:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:31:55: #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 06:31:55: #1 tags after filtering in treatment: 13263095 INFO @ Mon, 03 Jun 2019 06:31:55: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 03 Jun 2019 06:31:55: #1 finished! INFO @ Mon, 03 Jun 2019 06:31:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:31:56: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:31:56: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:31:56: #1 total tags in treatment: 15726030 INFO @ Mon, 03 Jun 2019 06:31:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:31:56: #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 06:31:56: #1 tags after filtering in treatment: 13263095 INFO @ Mon, 03 Jun 2019 06:31:56: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 03 Jun 2019 06:31:56: #1 finished! INFO @ Mon, 03 Jun 2019 06:31:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:31:57: #2 number of paired peaks: 7630 INFO @ Mon, 03 Jun 2019 06:31:57: start model_add_line... INFO @ Mon, 03 Jun 2019 06:31:57: start X-correlation... INFO @ Mon, 03 Jun 2019 06:31:57: end of X-cor INFO @ Mon, 03 Jun 2019 06:31:57: #2 finished! INFO @ Mon, 03 Jun 2019 06:31:57: #2 predicted fragment length is 164 bps INFO @ Mon, 03 Jun 2019 06:31:57: #2 alternative fragment length(s) may be 2,164 bps INFO @ Mon, 03 Jun 2019 06:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.20_model.r INFO @ Mon, 03 Jun 2019 06:31:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:31:58: #2 number of paired peaks: 7630 INFO @ Mon, 03 Jun 2019 06:31:58: start model_add_line... INFO @ Mon, 03 Jun 2019 06:31:59: start X-correlation... INFO @ Mon, 03 Jun 2019 06:31:59: end of X-cor INFO @ Mon, 03 Jun 2019 06:31:59: #2 finished! INFO @ Mon, 03 Jun 2019 06:31:59: #2 predicted fragment length is 164 bps INFO @ Mon, 03 Jun 2019 06:31:59: #2 alternative fragment length(s) may be 2,164 bps INFO @ Mon, 03 Jun 2019 06:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.10_model.r INFO @ Mon, 03 Jun 2019 06:31:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:32:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:32:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.05_summits.bed INFO @ Mon, 03 Jun 2019 06:32:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2094 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:32:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.20_summits.bed INFO @ Mon, 03 Jun 2019 06:33:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:33:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:33:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:33:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197561/SRX197561.10_summits.bed INFO @ Mon, 03 Jun 2019 06:33:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (940 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。