Job ID = 1294963 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:55:27 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' 2019-06-03T01:55:27 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/sra11/SRR/000849/SRR870213' 2019-06-03T01:55:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870213' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T01:55:36 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T02:01:26 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 ) 2019-06-03T02:05:26 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' 2019-06-03T02:05:26 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/sra11/SRR/000849/SRR870213' 2019-06-03T02:05:35 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR870213', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 18,433,026 reads read : 18,433,026 reads written : 18,433,026 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: 00:00:01 Multiseed full-index search: 00:08:07 18433026 reads; of these: 18433026 (100.00%) were unpaired; of these: 2118596 (11.49%) aligned 0 times 11473061 (62.24%) aligned exactly 1 time 4841369 (26.26%) aligned >1 times 88.51% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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_rmdupse_core] 3103896 / 16314430 = 0.1903 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 11:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.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 11:28:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:28:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.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 11:28:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:28:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.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 11:28:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:28:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:28:13: 1000000 INFO @ Mon, 03 Jun 2019 11:28:13: 1000000 INFO @ Mon, 03 Jun 2019 11:28:13: 1000000 INFO @ Mon, 03 Jun 2019 11:28:20: 2000000 INFO @ Mon, 03 Jun 2019 11:28:21: 2000000 INFO @ Mon, 03 Jun 2019 11:28:21: 2000000 INFO @ Mon, 03 Jun 2019 11:28:28: 3000000 INFO @ Mon, 03 Jun 2019 11:28:28: 3000000 INFO @ Mon, 03 Jun 2019 11:28:29: 3000000 INFO @ Mon, 03 Jun 2019 11:28:35: 4000000 INFO @ Mon, 03 Jun 2019 11:28:35: 4000000 INFO @ Mon, 03 Jun 2019 11:28:36: 4000000 INFO @ Mon, 03 Jun 2019 11:28:42: 5000000 INFO @ Mon, 03 Jun 2019 11:28:43: 5000000 INFO @ Mon, 03 Jun 2019 11:28:44: 5000000 INFO @ Mon, 03 Jun 2019 11:28:50: 6000000 INFO @ Mon, 03 Jun 2019 11:28:50: 6000000 INFO @ Mon, 03 Jun 2019 11:28:51: 6000000 INFO @ Mon, 03 Jun 2019 11:28:57: 7000000 INFO @ Mon, 03 Jun 2019 11:28:57: 7000000 INFO @ Mon, 03 Jun 2019 11:28:59: 7000000 INFO @ Mon, 03 Jun 2019 11:29:04: 8000000 INFO @ Mon, 03 Jun 2019 11:29:04: 8000000 INFO @ Mon, 03 Jun 2019 11:29:07: 8000000 INFO @ Mon, 03 Jun 2019 11:29:11: 9000000 INFO @ Mon, 03 Jun 2019 11:29:12: 9000000 INFO @ Mon, 03 Jun 2019 11:29:14: 9000000 INFO @ Mon, 03 Jun 2019 11:29:19: 10000000 INFO @ Mon, 03 Jun 2019 11:29:19: 10000000 INFO @ Mon, 03 Jun 2019 11:29:22: 10000000 INFO @ Mon, 03 Jun 2019 11:29:26: 11000000 INFO @ Mon, 03 Jun 2019 11:29:26: 11000000 INFO @ Mon, 03 Jun 2019 11:29:29: 11000000 INFO @ Mon, 03 Jun 2019 11:29:33: 12000000 INFO @ Mon, 03 Jun 2019 11:29:33: 12000000 INFO @ Mon, 03 Jun 2019 11:29:37: 12000000 INFO @ Mon, 03 Jun 2019 11:29:40: 13000000 INFO @ Mon, 03 Jun 2019 11:29:40: 13000000 INFO @ Mon, 03 Jun 2019 11:29:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:29:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:29:41: #1 total tags in treatment: 13210534 INFO @ Mon, 03 Jun 2019 11:29:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:41: #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 11:29:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:29:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:29:41: #1 total tags in treatment: 13210534 INFO @ Mon, 03 Jun 2019 11:29:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:41: #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 11:29:42: #1 tags after filtering in treatment: 13210534 INFO @ Mon, 03 Jun 2019 11:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:42: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:42: #1 tags after filtering in treatment: 13210534 INFO @ Mon, 03 Jun 2019 11:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:42: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:43: #2 number of paired peaks: 373 WARNING @ Mon, 03 Jun 2019 11:29:43: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Mon, 03 Jun 2019 11:29:43: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:43: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:43: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:43: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:43: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:29:43: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.10_model.r WARNING @ Mon, 03 Jun 2019 11:29:43: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:29:43: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:29:43: #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 11:29:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:29:43: #2 number of paired peaks: 373 WARNING @ Mon, 03 Jun 2019 11:29:43: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Mon, 03 Jun 2019 11:29:43: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:43: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:43: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:43: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:43: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:29:43: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.05_model.r WARNING @ Mon, 03 Jun 2019 11:29:43: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:29:43: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:29:43: #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 11:29:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:29:44: 13000000 INFO @ Mon, 03 Jun 2019 11:29:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:29:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:29:46: #1 total tags in treatment: 13210534 INFO @ Mon, 03 Jun 2019 11:29:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:46: #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 11:29:46: #1 tags after filtering in treatment: 13210534 INFO @ Mon, 03 Jun 2019 11:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:46: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:48: #2 number of paired peaks: 373 WARNING @ Mon, 03 Jun 2019 11:29:48: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Mon, 03 Jun 2019 11:29:48: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:48: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:48: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:48: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:48: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:29:48: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.20_model.r WARNING @ Mon, 03 Jun 2019 11:29:48: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:29:48: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:29:48: #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 11:29:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:30:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:30:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.05_summits.bed INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:30:35: Done! INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.10_summits.bed INFO @ Mon, 03 Jun 2019 11:30:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2131 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1752 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:30:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:30:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:30:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288024/SRX288024.20_summits.bed INFO @ Mon, 03 Jun 2019 11:30:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1241 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。