Job ID = 2010642 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:44:03 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 ) 2019-07-05T14:44:03 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.80' 2019-07-05T14:44:03 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' (130.14.250.24) from '172.19.7.80' spots read : 1,797,925 reads read : 3,595,850 reads written : 3,595,850 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:01 1797925 reads; of these: 1797925 (100.00%) were paired; of these: 1021004 (56.79%) aligned concordantly 0 times 599826 (33.36%) aligned concordantly exactly 1 time 177095 (9.85%) aligned concordantly >1 times ---- 1021004 pairs aligned concordantly 0 times; of these: 7820 (0.77%) aligned discordantly 1 time ---- 1013184 pairs aligned 0 times concordantly or discordantly; of these: 2026368 mates make up the pairs; of these: 1876996 (92.63%) aligned 0 times 113076 (5.58%) aligned exactly 1 time 36296 (1.79%) aligned >1 times 47.80% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 407940 / 781818 = 0.5218 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 @ Fri, 05 Jul 2019 23:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:49:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:49:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:49:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:49:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:49:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:49:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:07: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:50:07: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:50:07: #1 total tags in treatment: 372160 INFO @ Fri, 05 Jul 2019 23:50:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:50:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:50:07: #1 tags after filtering in treatment: 275171 INFO @ Fri, 05 Jul 2019 23:50:07: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:50:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:50:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:50:07: #2 number of paired peaks: 200 WARNING @ Fri, 05 Jul 2019 23:50:07: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Fri, 05 Jul 2019 23:50:07: start model_add_line... INFO @ Fri, 05 Jul 2019 23:50:07: start X-correlation... INFO @ Fri, 05 Jul 2019 23:50:07: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:50:07: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:50:07: #1 total tags in treatment: 372160 INFO @ Fri, 05 Jul 2019 23:50:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:50:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:50:07: #1 tags after filtering in treatment: 275171 INFO @ Fri, 05 Jul 2019 23:50:07: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:50:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:50:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:50:07: end of X-cor INFO @ Fri, 05 Jul 2019 23:50:07: #2 finished! INFO @ Fri, 05 Jul 2019 23:50:07: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 23:50:07: #2 alternative fragment length(s) may be 249 bps INFO @ Fri, 05 Jul 2019 23:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.10_model.r INFO @ Fri, 05 Jul 2019 23:50:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:50:07: #2 number of paired peaks: 200 WARNING @ Fri, 05 Jul 2019 23:50:07: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Fri, 05 Jul 2019 23:50:07: start model_add_line... INFO @ Fri, 05 Jul 2019 23:50:07: start X-correlation... INFO @ Fri, 05 Jul 2019 23:50:07: end of X-cor INFO @ Fri, 05 Jul 2019 23:50:07: #2 finished! INFO @ Fri, 05 Jul 2019 23:50:07: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 23:50:07: #2 alternative fragment length(s) may be 249 bps INFO @ Fri, 05 Jul 2019 23:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.05_model.r INFO @ Fri, 05 Jul 2019 23:50:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:50:08: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:50:08: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:50:08: #1 total tags in treatment: 372160 INFO @ Fri, 05 Jul 2019 23:50:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:50:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:50:08: #1 tags after filtering in treatment: 275171 INFO @ Fri, 05 Jul 2019 23:50:08: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:50:08: #1 finished! INFO @ Fri, 05 Jul 2019 23:50:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:50:08: #2 number of paired peaks: 200 WARNING @ Fri, 05 Jul 2019 23:50:08: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Fri, 05 Jul 2019 23:50:08: start model_add_line... INFO @ Fri, 05 Jul 2019 23:50:08: start X-correlation... INFO @ Fri, 05 Jul 2019 23:50:08: end of X-cor INFO @ Fri, 05 Jul 2019 23:50:08: #2 finished! INFO @ Fri, 05 Jul 2019 23:50:08: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 23:50:08: #2 alternative fragment length(s) may be 249 bps INFO @ Fri, 05 Jul 2019 23:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.20_model.r INFO @ Fri, 05 Jul 2019 23:50:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:50:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:50:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:50:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.10_summits.bed INFO @ Fri, 05 Jul 2019 23:50:09: Done! INFO @ Fri, 05 Jul 2019 23:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.05_summits.bed INFO @ Fri, 05 Jul 2019 23:50:09: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 4 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 23:50:09: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:50:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:50:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:50:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386370/SRX386370.20_summits.bed INFO @ Fri, 05 Jul 2019 23:50:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。