Job ID = 1293862 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:48:38 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 ) 2019-06-02T17:48:38 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.69' 2019-06-02T17:48:38 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' (130.14.250.25) from '172.19.7.69' 2019-06-02T17:48:38 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/SRR2546859/SRR2546859.1' 2019-06-02T17:48:38 fasterq-dump.2.9.6 err: invalid accession 'SRR2546859' spots read : 9,520,218 reads read : 9,520,218 reads written : 9,520,218 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: 00:03:51 9520218 reads; of these: 9520218 (100.00%) were unpaired; of these: 1185960 (12.46%) aligned 0 times 5768040 (60.59%) aligned exactly 1 time 2566218 (26.96%) aligned >1 times 87.54% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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_rmdupse_core] 3582969 / 8334258 = 0.4299 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 02:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.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 02:56:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:56:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.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 02:56:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:56:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.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 02:56:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:56:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:56:55: 1000000 INFO @ Mon, 03 Jun 2019 02:56:57: 1000000 INFO @ Mon, 03 Jun 2019 02:56:57: 1000000 INFO @ Mon, 03 Jun 2019 02:57:05: 2000000 INFO @ Mon, 03 Jun 2019 02:57:08: 2000000 INFO @ Mon, 03 Jun 2019 02:57:08: 2000000 INFO @ Mon, 03 Jun 2019 02:57:14: 3000000 INFO @ Mon, 03 Jun 2019 02:57:19: 3000000 INFO @ Mon, 03 Jun 2019 02:57:19: 3000000 INFO @ Mon, 03 Jun 2019 02:57:23: 4000000 INFO @ Mon, 03 Jun 2019 02:57:30: 4000000 INFO @ Mon, 03 Jun 2019 02:57:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:57:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:57:30: #1 total tags in treatment: 4751289 INFO @ Mon, 03 Jun 2019 02:57:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:57:30: #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 02:57:30: 4000000 INFO @ Mon, 03 Jun 2019 02:57:30: #1 tags after filtering in treatment: 4751289 INFO @ Mon, 03 Jun 2019 02:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:57:30: #1 finished! INFO @ Mon, 03 Jun 2019 02:57:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:57:31: #2 number of paired peaks: 2175 INFO @ Mon, 03 Jun 2019 02:57:31: start model_add_line... INFO @ Mon, 03 Jun 2019 02:57:31: start X-correlation... INFO @ Mon, 03 Jun 2019 02:57:31: end of X-cor INFO @ Mon, 03 Jun 2019 02:57:31: #2 finished! INFO @ Mon, 03 Jun 2019 02:57:31: #2 predicted fragment length is 73 bps INFO @ Mon, 03 Jun 2019 02:57:31: #2 alternative fragment length(s) may be 73 bps INFO @ Mon, 03 Jun 2019 02:57:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.10_model.r WARNING @ Mon, 03 Jun 2019 02:57:31: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:57:31: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Mon, 03 Jun 2019 02:57:31: #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 02:57:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:57:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:57:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:57:37: #1 total tags in treatment: 4751289 INFO @ Mon, 03 Jun 2019 02:57:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:57:37: #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 02:57:38: #1 tags after filtering in treatment: 4751289 INFO @ Mon, 03 Jun 2019 02:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:57:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:57:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:57:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:57:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:57:38: #1 total tags in treatment: 4751289 INFO @ Mon, 03 Jun 2019 02:57:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:57:38: #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 02:57:38: #1 tags after filtering in treatment: 4751289 INFO @ Mon, 03 Jun 2019 02:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:57:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:57:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:57:38: #2 number of paired peaks: 2175 INFO @ Mon, 03 Jun 2019 02:57:38: start model_add_line... INFO @ Mon, 03 Jun 2019 02:57:38: start X-correlation... INFO @ Mon, 03 Jun 2019 02:57:38: end of X-cor INFO @ Mon, 03 Jun 2019 02:57:38: #2 finished! INFO @ Mon, 03 Jun 2019 02:57:38: #2 predicted fragment length is 73 bps INFO @ Mon, 03 Jun 2019 02:57:38: #2 alternative fragment length(s) may be 73 bps INFO @ Mon, 03 Jun 2019 02:57:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.20_model.r WARNING @ Mon, 03 Jun 2019 02:57:38: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:57:38: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Mon, 03 Jun 2019 02:57:38: #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 02:57:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:57:38: #2 number of paired peaks: 2175 INFO @ Mon, 03 Jun 2019 02:57:38: start model_add_line... INFO @ Mon, 03 Jun 2019 02:57:39: start X-correlation... INFO @ Mon, 03 Jun 2019 02:57:39: end of X-cor INFO @ Mon, 03 Jun 2019 02:57:39: #2 finished! INFO @ Mon, 03 Jun 2019 02:57:39: #2 predicted fragment length is 73 bps INFO @ Mon, 03 Jun 2019 02:57:39: #2 alternative fragment length(s) may be 73 bps INFO @ Mon, 03 Jun 2019 02:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.05_model.r WARNING @ Mon, 03 Jun 2019 02:57:39: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:57:39: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Mon, 03 Jun 2019 02:57:39: #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 02:57:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:57:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:57:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:57:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.10_summits.bed INFO @ Mon, 03 Jun 2019 02:57:53: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1282 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:57:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.05_summits.bed INFO @ Mon, 03 Jun 2019 02:58:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2564 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299940/SRX1299940.20_summits.bed INFO @ Mon, 03 Jun 2019 02:58:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (569 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。