Job ID = 1295395 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:25:34 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T04:25:34 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra33/SRR/000930/SRR952862' 2019-06-03T04:25:44 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR952862' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T04:25:44 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T04:27:14 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 ) 2019-06-03T04:27:14 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 ) 2019-06-03T04:27:14 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 : 25,162,813 reads read : 25,162,813 reads written : 25,162,813 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: 00:10:25 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1369040 (5.44%) aligned 0 times 16619196 (66.05%) aligned exactly 1 time 7174577 (28.51%) aligned >1 times 94.56% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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 12 files... [bam_rmdupse_core] 5652193 / 23793773 = 0.2375 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 14:09:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.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 14:09:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:09:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.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 14:09:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:09:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.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 14:09:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:09:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:09:12: 1000000 INFO @ Mon, 03 Jun 2019 14:09:13: 1000000 INFO @ Mon, 03 Jun 2019 14:09:14: 1000000 INFO @ Mon, 03 Jun 2019 14:09:19: 2000000 INFO @ Mon, 03 Jun 2019 14:09:20: 2000000 INFO @ Mon, 03 Jun 2019 14:09:23: 2000000 INFO @ Mon, 03 Jun 2019 14:09:27: 3000000 INFO @ Mon, 03 Jun 2019 14:09:28: 3000000 INFO @ Mon, 03 Jun 2019 14:09:32: 3000000 INFO @ Mon, 03 Jun 2019 14:09:34: 4000000 INFO @ Mon, 03 Jun 2019 14:09:35: 4000000 INFO @ Mon, 03 Jun 2019 14:09:41: 4000000 INFO @ Mon, 03 Jun 2019 14:09:41: 5000000 INFO @ Mon, 03 Jun 2019 14:09:42: 5000000 INFO @ Mon, 03 Jun 2019 14:09:48: 6000000 INFO @ Mon, 03 Jun 2019 14:09:50: 6000000 INFO @ Mon, 03 Jun 2019 14:09:50: 5000000 INFO @ Mon, 03 Jun 2019 14:09:55: 7000000 INFO @ Mon, 03 Jun 2019 14:09:57: 7000000 INFO @ Mon, 03 Jun 2019 14:09:59: 6000000 INFO @ Mon, 03 Jun 2019 14:10:03: 8000000 INFO @ Mon, 03 Jun 2019 14:10:05: 8000000 INFO @ Mon, 03 Jun 2019 14:10:07: 7000000 INFO @ Mon, 03 Jun 2019 14:10:10: 9000000 INFO @ Mon, 03 Jun 2019 14:10:13: 9000000 INFO @ Mon, 03 Jun 2019 14:10:16: 8000000 INFO @ Mon, 03 Jun 2019 14:10:17: 10000000 INFO @ Mon, 03 Jun 2019 14:10:20: 10000000 INFO @ Mon, 03 Jun 2019 14:10:24: 11000000 INFO @ Mon, 03 Jun 2019 14:10:24: 9000000 INFO @ Mon, 03 Jun 2019 14:10:27: 11000000 INFO @ Mon, 03 Jun 2019 14:10:31: 12000000 INFO @ Mon, 03 Jun 2019 14:10:33: 10000000 INFO @ Mon, 03 Jun 2019 14:10:35: 12000000 INFO @ Mon, 03 Jun 2019 14:10:38: 13000000 INFO @ Mon, 03 Jun 2019 14:10:42: 11000000 INFO @ Mon, 03 Jun 2019 14:10:42: 13000000 INFO @ Mon, 03 Jun 2019 14:10:45: 14000000 INFO @ Mon, 03 Jun 2019 14:10:50: 12000000 INFO @ Mon, 03 Jun 2019 14:10:50: 14000000 INFO @ Mon, 03 Jun 2019 14:10:52: 15000000 INFO @ Mon, 03 Jun 2019 14:10:58: 15000000 INFO @ Mon, 03 Jun 2019 14:10:58: 13000000 INFO @ Mon, 03 Jun 2019 14:10:59: 16000000 INFO @ Mon, 03 Jun 2019 14:11:05: 16000000 INFO @ Mon, 03 Jun 2019 14:11:06: 14000000 INFO @ Mon, 03 Jun 2019 14:11:06: 17000000 INFO @ Mon, 03 Jun 2019 14:11:13: 17000000 INFO @ Mon, 03 Jun 2019 14:11:14: 18000000 INFO @ Mon, 03 Jun 2019 14:11:15: 15000000 INFO @ Mon, 03 Jun 2019 14:11:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:11:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:11:15: #1 total tags in treatment: 18141580 INFO @ Mon, 03 Jun 2019 14:11:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:11:15: #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 14:11:15: #1 tags after filtering in treatment: 18141580 INFO @ Mon, 03 Jun 2019 14:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:11:15: #1 finished! INFO @ Mon, 03 Jun 2019 14:11:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:11:17: #2 number of paired peaks: 121 WARNING @ Mon, 03 Jun 2019 14:11:17: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 03 Jun 2019 14:11:17: start model_add_line... INFO @ Mon, 03 Jun 2019 14:11:17: start X-correlation... INFO @ Mon, 03 Jun 2019 14:11:17: end of X-cor INFO @ Mon, 03 Jun 2019 14:11:17: #2 finished! INFO @ Mon, 03 Jun 2019 14:11:17: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 14:11:17: #2 alternative fragment length(s) may be 2,12,51,161,169,174,183,192,414,495,530,559,561,568,582 bps INFO @ Mon, 03 Jun 2019 14:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.05_model.r WARNING @ Mon, 03 Jun 2019 14:11:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:11:17: #2 You may need to consider one of the other alternative d(s): 2,12,51,161,169,174,183,192,414,495,530,559,561,568,582 WARNING @ Mon, 03 Jun 2019 14:11:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 14:11:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:11:20: 18000000 INFO @ Mon, 03 Jun 2019 14:11:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:11:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:11:22: #1 total tags in treatment: 18141580 INFO @ Mon, 03 Jun 2019 14:11:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:11:22: #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 14:11:22: #1 tags after filtering in treatment: 18141580 INFO @ Mon, 03 Jun 2019 14:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:11:22: #1 finished! INFO @ Mon, 03 Jun 2019 14:11:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:11:23: 16000000 INFO @ Mon, 03 Jun 2019 14:11:24: #2 number of paired peaks: 121 WARNING @ Mon, 03 Jun 2019 14:11:24: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 03 Jun 2019 14:11:24: start model_add_line... INFO @ Mon, 03 Jun 2019 14:11:24: start X-correlation... INFO @ Mon, 03 Jun 2019 14:11:24: end of X-cor INFO @ Mon, 03 Jun 2019 14:11:24: #2 finished! INFO @ Mon, 03 Jun 2019 14:11:24: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 14:11:24: #2 alternative fragment length(s) may be 2,12,51,161,169,174,183,192,414,495,530,559,561,568,582 bps INFO @ Mon, 03 Jun 2019 14:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.20_model.r WARNING @ Mon, 03 Jun 2019 14:11:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:11:24: #2 You may need to consider one of the other alternative d(s): 2,12,51,161,169,174,183,192,414,495,530,559,561,568,582 WARNING @ Mon, 03 Jun 2019 14:11:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 14:11:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:11:32: 17000000 INFO @ Mon, 03 Jun 2019 14:11:40: 18000000 INFO @ Mon, 03 Jun 2019 14:11:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:11:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:11:41: #1 total tags in treatment: 18141580 INFO @ Mon, 03 Jun 2019 14:11:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:11:41: #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 14:11:42: #1 tags after filtering in treatment: 18141580 INFO @ Mon, 03 Jun 2019 14:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:11:42: #1 finished! INFO @ Mon, 03 Jun 2019 14:11:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:11:43: #2 number of paired peaks: 121 WARNING @ Mon, 03 Jun 2019 14:11:43: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 03 Jun 2019 14:11:43: start model_add_line... INFO @ Mon, 03 Jun 2019 14:11:44: start X-correlation... INFO @ Mon, 03 Jun 2019 14:11:44: end of X-cor INFO @ Mon, 03 Jun 2019 14:11:44: #2 finished! INFO @ Mon, 03 Jun 2019 14:11:44: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 14:11:44: #2 alternative fragment length(s) may be 2,12,51,161,169,174,183,192,414,495,530,559,561,568,582 bps INFO @ Mon, 03 Jun 2019 14:11:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.10_model.r WARNING @ Mon, 03 Jun 2019 14:11:44: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:11:44: #2 You may need to consider one of the other alternative d(s): 2,12,51,161,169,174,183,192,414,495,530,559,561,568,582 WARNING @ Mon, 03 Jun 2019 14:11:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 14:11:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:12:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:12:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.05_summits.bed INFO @ Mon, 03 Jun 2019 14:12:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2372 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:12:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.20_summits.bed INFO @ Mon, 03 Jun 2019 14:12:37: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335520/SRX335520.10_summits.bed INFO @ Mon, 03 Jun 2019 14:13:00: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1149 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。