Job ID = 1303283 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:15:22 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' 2019-06-03T11:15:22 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/sra72/SRR/007917/SRR8107294' 2019-06-03T11:15:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8107294' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T11:17:38 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 ) 2019-06-03T11:17:38 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 ) 2019-06-03T11:17:38 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 ) 2019-06-03T11:24:10 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 ) 2019-06-03T11:24:10 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 : 15,640,900 reads read : 15,640,900 reads written : 15,640,900 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: 00:06:16 15640900 reads; of these: 15640900 (100.00%) were unpaired; of these: 3274137 (20.93%) aligned 0 times 9000972 (57.55%) aligned exactly 1 time 3365791 (21.52%) aligned >1 times 79.07% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 8317101 / 12366763 = 0.6725 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 20:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.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 20:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.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 20:34:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:34:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:34:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:34:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.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 20:34:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:34:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:35:03: 1000000 INFO @ Mon, 03 Jun 2019 20:35:03: 1000000 INFO @ Mon, 03 Jun 2019 20:35:06: 1000000 INFO @ Mon, 03 Jun 2019 20:35:11: 2000000 INFO @ Mon, 03 Jun 2019 20:35:11: 2000000 INFO @ Mon, 03 Jun 2019 20:35:16: 2000000 INFO @ Mon, 03 Jun 2019 20:35:19: 3000000 INFO @ Mon, 03 Jun 2019 20:35:19: 3000000 INFO @ Mon, 03 Jun 2019 20:35:25: 3000000 INFO @ Mon, 03 Jun 2019 20:35:27: 4000000 INFO @ Mon, 03 Jun 2019 20:35:27: 4000000 INFO @ Mon, 03 Jun 2019 20:35:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:35:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:35:28: #1 total tags in treatment: 4049662 INFO @ Mon, 03 Jun 2019 20:35:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:35:28: #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 20:35:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:35:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:35:28: #1 total tags in treatment: 4049662 INFO @ Mon, 03 Jun 2019 20:35:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:35:28: #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 20:35:28: #1 tags after filtering in treatment: 4049662 INFO @ Mon, 03 Jun 2019 20:35:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:35:28: #1 finished! INFO @ Mon, 03 Jun 2019 20:35:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:35:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:35:28: #1 tags after filtering in treatment: 4049662 INFO @ Mon, 03 Jun 2019 20:35:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:35:28: #1 finished! INFO @ Mon, 03 Jun 2019 20:35:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:35:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:35:28: #2 number of paired peaks: 953 WARNING @ Mon, 03 Jun 2019 20:35:28: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Mon, 03 Jun 2019 20:35:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:35:28: #2 number of paired peaks: 953 WARNING @ Mon, 03 Jun 2019 20:35:28: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Mon, 03 Jun 2019 20:35:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:35:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:35:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:35:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:35:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:35:28: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:35:28: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:35:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.20_model.r INFO @ Mon, 03 Jun 2019 20:35:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:35:28: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:35:28: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.05_model.r WARNING @ Mon, 03 Jun 2019 20:35:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:35:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:35:29: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:35:29: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:35:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Mon, 03 Jun 2019 20:35:29: #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 20:35:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:35:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:35:35: 4000000 INFO @ Mon, 03 Jun 2019 20:35:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:35:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:35:35: #1 total tags in treatment: 4049662 INFO @ Mon, 03 Jun 2019 20:35:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:35:35: #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 20:35:35: #1 tags after filtering in treatment: 4049662 INFO @ Mon, 03 Jun 2019 20:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:35:35: #1 finished! INFO @ Mon, 03 Jun 2019 20:35:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:35:36: #2 number of paired peaks: 953 WARNING @ Mon, 03 Jun 2019 20:35:36: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Mon, 03 Jun 2019 20:35:36: start model_add_line... INFO @ Mon, 03 Jun 2019 20:35:36: start X-correlation... INFO @ Mon, 03 Jun 2019 20:35:36: end of X-cor INFO @ Mon, 03 Jun 2019 20:35:36: #2 finished! INFO @ Mon, 03 Jun 2019 20:35:36: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:35:36: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:35:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.10_model.r WARNING @ Mon, 03 Jun 2019 20:35:36: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:35:36: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:35:36: #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 20:35:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:35:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:35:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.05_summits.bed INFO @ Mon, 03 Jun 2019 20:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:35:47: Done! INFO @ Mon, 03 Jun 2019 20:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.20_summits.bed INFO @ Mon, 03 Jun 2019 20:35:47: Done! pass1 - making usageList (8 chroms): 1 millis pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1039 records, 4 fields): 9 millis pass2 - checking and writing primary data (1568 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:35:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933903/SRX4933903.10_summits.bed INFO @ Mon, 03 Jun 2019 20:35:54: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (1315 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。