Job ID = 1307171 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:05:35 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' 2019-06-03T13:05:35 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/sos/sra-pub-run-2/SRR8433310/SRR8433310.1' 2019-06-03T13:05:35 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8433310' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:05:35 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:12:51 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 : 21,616,990 reads read : 43,233,980 reads written : 21,616,990 reads 0-length : 21,616,990 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: 00:11:27 21616990 reads; of these: 21616990 (100.00%) were unpaired; of these: 855441 (3.96%) aligned 0 times 16631466 (76.94%) aligned exactly 1 time 4130083 (19.11%) aligned >1 times 96.04% overall alignment rate Time searching: 00:11:27 Overall time: 00:11:27 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] 2113596 / 20761549 = 0.1018 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 22:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.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 22:43:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:43:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.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 22:43:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:43:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.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 22:43:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:43:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:43:36: 1000000 INFO @ Mon, 03 Jun 2019 22:43:36: 1000000 INFO @ Mon, 03 Jun 2019 22:43:37: 1000000 INFO @ Mon, 03 Jun 2019 22:43:45: 2000000 INFO @ Mon, 03 Jun 2019 22:43:45: 2000000 INFO @ Mon, 03 Jun 2019 22:43:47: 2000000 INFO @ Mon, 03 Jun 2019 22:43:54: 3000000 INFO @ Mon, 03 Jun 2019 22:43:55: 3000000 INFO @ Mon, 03 Jun 2019 22:43:57: 3000000 INFO @ Mon, 03 Jun 2019 22:44:03: 4000000 INFO @ Mon, 03 Jun 2019 22:44:04: 4000000 INFO @ Mon, 03 Jun 2019 22:44:07: 4000000 INFO @ Mon, 03 Jun 2019 22:44:11: 5000000 INFO @ Mon, 03 Jun 2019 22:44:13: 5000000 INFO @ Mon, 03 Jun 2019 22:44:17: 5000000 INFO @ Mon, 03 Jun 2019 22:44:20: 6000000 INFO @ Mon, 03 Jun 2019 22:44:22: 6000000 INFO @ Mon, 03 Jun 2019 22:44:27: 6000000 INFO @ Mon, 03 Jun 2019 22:44:28: 7000000 INFO @ Mon, 03 Jun 2019 22:44:31: 7000000 INFO @ Mon, 03 Jun 2019 22:44:36: 8000000 INFO @ Mon, 03 Jun 2019 22:44:37: 7000000 INFO @ Mon, 03 Jun 2019 22:44:40: 8000000 INFO @ Mon, 03 Jun 2019 22:44:46: 9000000 INFO @ Mon, 03 Jun 2019 22:44:49: 8000000 INFO @ Mon, 03 Jun 2019 22:44:50: 9000000 INFO @ Mon, 03 Jun 2019 22:44:56: 10000000 INFO @ Mon, 03 Jun 2019 22:45:00: 10000000 INFO @ Mon, 03 Jun 2019 22:45:02: 9000000 INFO @ Mon, 03 Jun 2019 22:45:05: 11000000 INFO @ Mon, 03 Jun 2019 22:45:08: 11000000 INFO @ Mon, 03 Jun 2019 22:45:12: 10000000 INFO @ Mon, 03 Jun 2019 22:45:13: 12000000 INFO @ Mon, 03 Jun 2019 22:45:17: 12000000 INFO @ Mon, 03 Jun 2019 22:45:22: 13000000 INFO @ Mon, 03 Jun 2019 22:45:23: 11000000 INFO @ Mon, 03 Jun 2019 22:45:26: 13000000 INFO @ Mon, 03 Jun 2019 22:45:30: 14000000 INFO @ Mon, 03 Jun 2019 22:45:33: 12000000 INFO @ Mon, 03 Jun 2019 22:45:36: 14000000 INFO @ Mon, 03 Jun 2019 22:45:39: 15000000 INFO @ Mon, 03 Jun 2019 22:45:44: 13000000 INFO @ Mon, 03 Jun 2019 22:45:45: 15000000 INFO @ Mon, 03 Jun 2019 22:45:47: 16000000 INFO @ Mon, 03 Jun 2019 22:45:54: 14000000 INFO @ Mon, 03 Jun 2019 22:45:54: 16000000 INFO @ Mon, 03 Jun 2019 22:45:56: 17000000 INFO @ Mon, 03 Jun 2019 22:46:03: 17000000 INFO @ Mon, 03 Jun 2019 22:46:04: 18000000 INFO @ Mon, 03 Jun 2019 22:46:05: 15000000 INFO @ Mon, 03 Jun 2019 22:46:10: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:46:10: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:46:10: #1 total tags in treatment: 18647953 INFO @ Mon, 03 Jun 2019 22:46:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:10: #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 22:46:10: #1 tags after filtering in treatment: 18647953 INFO @ Mon, 03 Jun 2019 22:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:10: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:12: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 22:46:12: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 22:46:12: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:12: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:12: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:12: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:12: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 22:46:12: #2 alternative fragment length(s) may be 4,86 bps INFO @ Mon, 03 Jun 2019 22:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.20_model.r WARNING @ Mon, 03 Jun 2019 22:46:12: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:46:12: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Mon, 03 Jun 2019 22:46:12: #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 22:46:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:12: 18000000 INFO @ Mon, 03 Jun 2019 22:46:16: 16000000 INFO @ Mon, 03 Jun 2019 22:46:17: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:46:17: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:46:17: #1 total tags in treatment: 18647953 INFO @ Mon, 03 Jun 2019 22:46:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:17: #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 22:46:18: #1 tags after filtering in treatment: 18647953 INFO @ Mon, 03 Jun 2019 22:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:18: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:19: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 22:46:19: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 22:46:19: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:20: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:20: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:20: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:20: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 22:46:20: #2 alternative fragment length(s) may be 4,86 bps INFO @ Mon, 03 Jun 2019 22:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.05_model.r WARNING @ Mon, 03 Jun 2019 22:46:20: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:46:20: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Mon, 03 Jun 2019 22:46:20: #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 22:46:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:27: 17000000 INFO @ Mon, 03 Jun 2019 22:46:37: 18000000 INFO @ Mon, 03 Jun 2019 22:46:43: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:46:43: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:46:43: #1 total tags in treatment: 18647953 INFO @ Mon, 03 Jun 2019 22:46:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:43: #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 22:46:44: #1 tags after filtering in treatment: 18647953 INFO @ Mon, 03 Jun 2019 22:46:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:44: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:45: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 22:46:45: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 22:46:45: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:46: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:46: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:46: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:46: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 22:46:46: #2 alternative fragment length(s) may be 4,86 bps INFO @ Mon, 03 Jun 2019 22:46:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.10_model.r WARNING @ Mon, 03 Jun 2019 22:46:46: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:46:46: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Mon, 03 Jun 2019 22:46:46: #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 22:46:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:47:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.20_summits.bed INFO @ Mon, 03 Jun 2019 22:47:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.05_summits.bed INFO @ Mon, 03 Jun 2019 22:47:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3478 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:47:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241029/SRX5241029.10_summits.bed INFO @ Mon, 03 Jun 2019 22:48:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (887 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。