Job ID = 1299555 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:28:04 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 ) 2019-06-03T09:28:04 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 ) 2019-06-03T09:28:04 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 ) 2019-06-03T09:28:04 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 ) 2019-06-03T09:29:44 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T09:30:48 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 ) 2019-06-03T09:31:41 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 : 14,904,493 reads read : 29,808,986 reads written : 29,808,986 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:40 14904493 reads; of these: 14904493 (100.00%) were paired; of these: 7057899 (47.35%) aligned concordantly 0 times 6057527 (40.64%) aligned concordantly exactly 1 time 1789067 (12.00%) aligned concordantly >1 times ---- 7057899 pairs aligned concordantly 0 times; of these: 170860 (2.42%) aligned discordantly 1 time ---- 6887039 pairs aligned 0 times concordantly or discordantly; of these: 13774078 mates make up the pairs; of these: 13402214 (97.30%) aligned 0 times 231550 (1.68%) aligned exactly 1 time 140314 (1.02%) aligned >1 times 55.04% overall alignment rate Time searching: 00:20:41 Overall time: 00:20:41 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 8 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] 1834140 / 8012864 = 0.2289 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 19:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.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 19:00:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:00:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.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 19:00:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:00:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.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 19:00:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:00:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:00:14: 1000000 INFO @ Mon, 03 Jun 2019 19:00:16: 1000000 INFO @ Mon, 03 Jun 2019 19:00:17: 1000000 INFO @ Mon, 03 Jun 2019 19:00:20: 2000000 INFO @ Mon, 03 Jun 2019 19:00:25: 2000000 INFO @ Mon, 03 Jun 2019 19:00:26: 2000000 INFO @ Mon, 03 Jun 2019 19:00:26: 3000000 INFO @ Mon, 03 Jun 2019 19:00:33: 4000000 INFO @ Mon, 03 Jun 2019 19:00:33: 3000000 INFO @ Mon, 03 Jun 2019 19:00:34: 3000000 INFO @ Mon, 03 Jun 2019 19:00:39: 5000000 INFO @ Mon, 03 Jun 2019 19:00:43: 4000000 INFO @ Mon, 03 Jun 2019 19:00:43: 4000000 INFO @ Mon, 03 Jun 2019 19:00:45: 6000000 INFO @ Mon, 03 Jun 2019 19:00:51: 7000000 INFO @ Mon, 03 Jun 2019 19:00:52: 5000000 INFO @ Mon, 03 Jun 2019 19:00:52: 5000000 INFO @ Mon, 03 Jun 2019 19:00:58: 8000000 INFO @ Mon, 03 Jun 2019 19:01:00: 6000000 INFO @ Mon, 03 Jun 2019 19:01:01: 6000000 INFO @ Mon, 03 Jun 2019 19:01:04: 9000000 INFO @ Mon, 03 Jun 2019 19:01:09: 7000000 INFO @ Mon, 03 Jun 2019 19:01:10: 7000000 INFO @ Mon, 03 Jun 2019 19:01:10: 10000000 INFO @ Mon, 03 Jun 2019 19:01:16: 11000000 INFO @ Mon, 03 Jun 2019 19:01:17: 8000000 INFO @ Mon, 03 Jun 2019 19:01:18: 8000000 INFO @ Mon, 03 Jun 2019 19:01:22: 12000000 INFO @ Mon, 03 Jun 2019 19:01:26: 9000000 INFO @ Mon, 03 Jun 2019 19:01:27: 9000000 INFO @ Mon, 03 Jun 2019 19:01:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:01:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:01:27: #1 total tags in treatment: 6039722 INFO @ Mon, 03 Jun 2019 19:01:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:01:27: #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 19:01:27: #1 tags after filtering in treatment: 5893423 INFO @ Mon, 03 Jun 2019 19:01:27: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 19:01:27: #1 finished! INFO @ Mon, 03 Jun 2019 19:01:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:01:28: #2 number of paired peaks: 333 WARNING @ Mon, 03 Jun 2019 19:01:28: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Mon, 03 Jun 2019 19:01:28: start model_add_line... INFO @ Mon, 03 Jun 2019 19:01:28: start X-correlation... INFO @ Mon, 03 Jun 2019 19:01:28: end of X-cor INFO @ Mon, 03 Jun 2019 19:01:28: #2 finished! INFO @ Mon, 03 Jun 2019 19:01:28: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 19:01:28: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 19:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.05_model.r INFO @ Mon, 03 Jun 2019 19:01:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:01:34: 10000000 INFO @ Mon, 03 Jun 2019 19:01:36: 10000000 INFO @ Mon, 03 Jun 2019 19:01:43: 11000000 INFO @ Mon, 03 Jun 2019 19:01:44: 11000000 INFO @ Mon, 03 Jun 2019 19:01:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:01:51: 12000000 INFO @ Mon, 03 Jun 2019 19:01:53: 12000000 INFO @ Mon, 03 Jun 2019 19:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.05_summits.bed INFO @ Mon, 03 Jun 2019 19:01:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1124 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:01:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:01:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:01:57: #1 total tags in treatment: 6039722 INFO @ Mon, 03 Jun 2019 19:01:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:01:57: #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 19:01:57: #1 tags after filtering in treatment: 5893423 INFO @ Mon, 03 Jun 2019 19:01:57: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 19:01:57: #1 finished! INFO @ Mon, 03 Jun 2019 19:01:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:01:58: #2 number of paired peaks: 333 WARNING @ Mon, 03 Jun 2019 19:01:58: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Mon, 03 Jun 2019 19:01:58: start model_add_line... INFO @ Mon, 03 Jun 2019 19:01:58: start X-correlation... INFO @ Mon, 03 Jun 2019 19:01:58: end of X-cor INFO @ Mon, 03 Jun 2019 19:01:58: #2 finished! INFO @ Mon, 03 Jun 2019 19:01:58: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 19:01:58: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 19:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.10_model.r INFO @ Mon, 03 Jun 2019 19:01:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:01:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:01:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:01:59: #1 total tags in treatment: 6039722 INFO @ Mon, 03 Jun 2019 19:01:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:01:59: #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 19:01:59: #1 tags after filtering in treatment: 5893423 INFO @ Mon, 03 Jun 2019 19:01:59: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 19:01:59: #1 finished! INFO @ Mon, 03 Jun 2019 19:01:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:02:00: #2 number of paired peaks: 333 WARNING @ Mon, 03 Jun 2019 19:02:00: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Mon, 03 Jun 2019 19:02:00: start model_add_line... INFO @ Mon, 03 Jun 2019 19:02:00: start X-correlation... INFO @ Mon, 03 Jun 2019 19:02:00: end of X-cor INFO @ Mon, 03 Jun 2019 19:02:00: #2 finished! INFO @ Mon, 03 Jun 2019 19:02:00: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 19:02:00: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 19:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.20_model.r INFO @ Mon, 03 Jun 2019 19:02:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:02:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:02:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.10_summits.bed INFO @ Mon, 03 Jun 2019 19:02:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474590/SRX474590.20_summits.bed INFO @ Mon, 03 Jun 2019 19:02:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。