Job ID = 2589971 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:52:31 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T09:52:31 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.56' 2019-08-12T09:52:31 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.26) from '172.19.7.56' 2019-08-12T09:52:31 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1163568/SRR1163568.1' 2019-08-12T09:52:42 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR1163568', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 11,726,087 reads read : 11,726,087 reads written : 11,726,087 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163568.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:12 11726087 reads; of these: 11726087 (100.00%) were unpaired; of these: 483198 (4.12%) aligned 0 times 9732594 (83.00%) aligned exactly 1 time 1510295 (12.88%) aligned >1 times 95.88% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 7097366 / 11242889 = 0.6313 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, 12 Aug 2019 18:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 18:59:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:59:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 18:59:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:59:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 18:59:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:59:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:59:18: 1000000 INFO @ Mon, 12 Aug 2019 18:59:20: 1000000 INFO @ Mon, 12 Aug 2019 18:59:21: 1000000 INFO @ Mon, 12 Aug 2019 18:59:25: 2000000 INFO @ Mon, 12 Aug 2019 18:59:28: 2000000 INFO @ Mon, 12 Aug 2019 18:59:30: 2000000 INFO @ Mon, 12 Aug 2019 18:59:32: 3000000 INFO @ Mon, 12 Aug 2019 18:59:36: 3000000 INFO @ Mon, 12 Aug 2019 18:59:39: 4000000 INFO @ Mon, 12 Aug 2019 18:59:39: 3000000 INFO @ Mon, 12 Aug 2019 18:59:40: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 18:59:40: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 18:59:40: #1 total tags in treatment: 4145523 INFO @ Mon, 12 Aug 2019 18:59:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:59:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:59:40: #1 tags after filtering in treatment: 4145523 INFO @ Mon, 12 Aug 2019 18:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:59:40: #1 finished! INFO @ Mon, 12 Aug 2019 18:59:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:59:40: #2 number of paired peaks: 508 WARNING @ Mon, 12 Aug 2019 18:59:40: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Mon, 12 Aug 2019 18:59:40: start model_add_line... INFO @ Mon, 12 Aug 2019 18:59:40: start X-correlation... INFO @ Mon, 12 Aug 2019 18:59:40: end of X-cor INFO @ Mon, 12 Aug 2019 18:59:40: #2 finished! INFO @ Mon, 12 Aug 2019 18:59:40: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 18:59:40: #2 alternative fragment length(s) may be 4,43 bps INFO @ Mon, 12 Aug 2019 18:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.05_model.r WARNING @ Mon, 12 Aug 2019 18:59:40: #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, 12 Aug 2019 18:59:40: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Mon, 12 Aug 2019 18:59:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:59:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:59:44: 4000000 INFO @ Mon, 12 Aug 2019 18:59:45: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 18:59:45: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 18:59:45: #1 total tags in treatment: 4145523 INFO @ Mon, 12 Aug 2019 18:59:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:59:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:59:45: #1 tags after filtering in treatment: 4145523 INFO @ Mon, 12 Aug 2019 18:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:59:45: #1 finished! INFO @ Mon, 12 Aug 2019 18:59:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:59:45: #2 number of paired peaks: 508 WARNING @ Mon, 12 Aug 2019 18:59:45: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Mon, 12 Aug 2019 18:59:45: start model_add_line... INFO @ Mon, 12 Aug 2019 18:59:45: start X-correlation... INFO @ Mon, 12 Aug 2019 18:59:45: end of X-cor INFO @ Mon, 12 Aug 2019 18:59:45: #2 finished! INFO @ Mon, 12 Aug 2019 18:59:45: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 18:59:45: #2 alternative fragment length(s) may be 4,43 bps INFO @ Mon, 12 Aug 2019 18:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.20_model.r WARNING @ Mon, 12 Aug 2019 18:59:45: #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, 12 Aug 2019 18:59:45: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Mon, 12 Aug 2019 18:59:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:59:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:59:48: 4000000 INFO @ Mon, 12 Aug 2019 18:59:49: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 18:59:49: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 18:59:49: #1 total tags in treatment: 4145523 INFO @ Mon, 12 Aug 2019 18:59:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:59:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:59:49: #1 tags after filtering in treatment: 4145523 INFO @ Mon, 12 Aug 2019 18:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:59:49: #1 finished! INFO @ Mon, 12 Aug 2019 18:59:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:59:50: #2 number of paired peaks: 508 WARNING @ Mon, 12 Aug 2019 18:59:50: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Mon, 12 Aug 2019 18:59:50: start model_add_line... INFO @ Mon, 12 Aug 2019 18:59:50: start X-correlation... INFO @ Mon, 12 Aug 2019 18:59:50: end of X-cor INFO @ Mon, 12 Aug 2019 18:59:50: #2 finished! INFO @ Mon, 12 Aug 2019 18:59:50: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 18:59:50: #2 alternative fragment length(s) may be 4,43 bps INFO @ Mon, 12 Aug 2019 18:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.10_model.r WARNING @ Mon, 12 Aug 2019 18:59:50: #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, 12 Aug 2019 18:59:50: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Mon, 12 Aug 2019 18:59:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:59:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:59:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:59:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:59:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.05_summits.bed INFO @ Mon, 12 Aug 2019 18:59:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:00:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.20_summits.bed INFO @ Mon, 12 Aug 2019 19:00:04: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466502/SRX466502.10_summits.bed INFO @ Mon, 12 Aug 2019 19:00:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (306 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。