Job ID = 1295238 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:50:17 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 ) 2019-06-03T03:50:17 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.84' 2019-06-03T03:50:17 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 '172.19.7.84' 2019-06-03T03:50:17 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/traces/sra13/SRR/000925/SRR947640' 2019-06-03T03:50:26 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR947640' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T03:50:26 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 11,861,028 reads read : 11,861,028 reads written : 11,861,028 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: 00:05:13 11861028 reads; of these: 11861028 (100.00%) were unpaired; of these: 1442467 (12.16%) aligned 0 times 6938480 (58.50%) aligned exactly 1 time 3480081 (29.34%) aligned >1 times 87.84% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3406944 / 10418561 = 0.3270 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 13:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.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 13:10:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:10:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.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 13:10:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:10:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.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 13:10:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:10:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:10:16: 1000000 INFO @ Mon, 03 Jun 2019 13:10:19: 1000000 INFO @ Mon, 03 Jun 2019 13:10:20: 1000000 INFO @ Mon, 03 Jun 2019 13:10:23: 2000000 INFO @ Mon, 03 Jun 2019 13:10:30: 2000000 INFO @ Mon, 03 Jun 2019 13:10:31: 3000000 INFO @ Mon, 03 Jun 2019 13:10:32: 2000000 INFO @ Mon, 03 Jun 2019 13:10:39: 4000000 INFO @ Mon, 03 Jun 2019 13:10:42: 3000000 INFO @ Mon, 03 Jun 2019 13:10:44: 3000000 INFO @ Mon, 03 Jun 2019 13:10:47: 5000000 INFO @ Mon, 03 Jun 2019 13:10:54: 4000000 INFO @ Mon, 03 Jun 2019 13:10:54: 6000000 INFO @ Mon, 03 Jun 2019 13:10:56: 4000000 INFO @ Mon, 03 Jun 2019 13:11:03: 7000000 INFO @ Mon, 03 Jun 2019 13:11:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:11:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:11:03: #1 total tags in treatment: 7011617 INFO @ Mon, 03 Jun 2019 13:11:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:11:03: #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 13:11:03: #1 tags after filtering in treatment: 7011617 INFO @ Mon, 03 Jun 2019 13:11:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:11:03: #1 finished! INFO @ Mon, 03 Jun 2019 13:11:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:11:04: #2 number of paired peaks: 399 WARNING @ Mon, 03 Jun 2019 13:11:04: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Mon, 03 Jun 2019 13:11:04: start model_add_line... INFO @ Mon, 03 Jun 2019 13:11:04: start X-correlation... INFO @ Mon, 03 Jun 2019 13:11:04: end of X-cor INFO @ Mon, 03 Jun 2019 13:11:04: #2 finished! INFO @ Mon, 03 Jun 2019 13:11:04: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:11:04: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 13:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.20_model.r WARNING @ Mon, 03 Jun 2019 13:11:04: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:11:04: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 13:11:04: #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 13:11:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:11:05: 5000000 INFO @ Mon, 03 Jun 2019 13:11:07: 5000000 INFO @ Mon, 03 Jun 2019 13:11:16: 6000000 INFO @ Mon, 03 Jun 2019 13:11:19: 6000000 INFO @ Mon, 03 Jun 2019 13:11:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:11:28: 7000000 INFO @ Mon, 03 Jun 2019 13:11:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:11:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:11:28: #1 total tags in treatment: 7011617 INFO @ Mon, 03 Jun 2019 13:11:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:11:28: #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 13:11:28: #1 tags after filtering in treatment: 7011617 INFO @ Mon, 03 Jun 2019 13:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:11:28: #1 finished! INFO @ Mon, 03 Jun 2019 13:11:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:11:29: #2 number of paired peaks: 399 WARNING @ Mon, 03 Jun 2019 13:11:29: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Mon, 03 Jun 2019 13:11:29: start model_add_line... INFO @ Mon, 03 Jun 2019 13:11:29: start X-correlation... INFO @ Mon, 03 Jun 2019 13:11:29: end of X-cor INFO @ Mon, 03 Jun 2019 13:11:29: #2 finished! INFO @ Mon, 03 Jun 2019 13:11:29: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:11:29: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 13:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.05_model.r WARNING @ Mon, 03 Jun 2019 13:11:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:11:29: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 13:11:29: #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 13:11:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:11:29: 7000000 INFO @ Mon, 03 Jun 2019 13:11:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:11:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:11:30: #1 total tags in treatment: 7011617 INFO @ Mon, 03 Jun 2019 13:11:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:11:30: #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 13:11:30: #1 tags after filtering in treatment: 7011617 INFO @ Mon, 03 Jun 2019 13:11:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:11:30: #1 finished! INFO @ Mon, 03 Jun 2019 13:11:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:11:30: #2 number of paired peaks: 399 WARNING @ Mon, 03 Jun 2019 13:11:30: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Mon, 03 Jun 2019 13:11:30: start model_add_line... INFO @ Mon, 03 Jun 2019 13:11:30: start X-correlation... INFO @ Mon, 03 Jun 2019 13:11:30: end of X-cor INFO @ Mon, 03 Jun 2019 13:11:30: #2 finished! INFO @ Mon, 03 Jun 2019 13:11:30: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:11:30: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 13:11:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.10_model.r WARNING @ Mon, 03 Jun 2019 13:11:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:11:30: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 13:11:30: #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 13:11:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:11:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:11:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:11:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.20_summits.bed INFO @ Mon, 03 Jun 2019 13:11:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:11:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:11:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.05_summits.bed INFO @ Mon, 03 Jun 2019 13:12:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4035 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331403/SRX331403.10_summits.bed INFO @ Mon, 03 Jun 2019 13:12:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1313 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。