Job ID = 2008165 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:31:44 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 8,727,258 reads read : 17,454,516 reads written : 17,454,516 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629083.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:13 8727258 reads; of these: 8727258 (100.00%) were paired; of these: 433772 (4.97%) aligned concordantly 0 times 7607331 (87.17%) aligned concordantly exactly 1 time 686155 (7.86%) aligned concordantly >1 times ---- 433772 pairs aligned concordantly 0 times; of these: 52355 (12.07%) aligned discordantly 1 time ---- 381417 pairs aligned 0 times concordantly or discordantly; of these: 762834 mates make up the pairs; of these: 693676 (90.93%) aligned 0 times 43502 (5.70%) aligned exactly 1 time 25656 (3.36%) aligned >1 times 96.03% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [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] 7814221 / 8332030 = 0.9379 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 17:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.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 17:41:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:41:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.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 17:41:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:41:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:41:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.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 17:41:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:41:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:41:58: 1000000 INFO @ Fri, 05 Jul 2019 17:41:58: 1000000 INFO @ Fri, 05 Jul 2019 17:41:59: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:41:59: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:41:59: #1 total tags in treatment: 520118 INFO @ Fri, 05 Jul 2019 17:41:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:41:59: #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 17:41:59: #1 tags after filtering in treatment: 441452 INFO @ Fri, 05 Jul 2019 17:41:59: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 17:41:59: #1 finished! INFO @ Fri, 05 Jul 2019 17:41:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:41:59: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 17:41:59: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 17:41:59: start model_add_line... INFO @ Fri, 05 Jul 2019 17:41:59: start X-correlation... INFO @ Fri, 05 Jul 2019 17:41:59: end of X-cor INFO @ Fri, 05 Jul 2019 17:41:59: #2 finished! INFO @ Fri, 05 Jul 2019 17:41:59: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 17:41:59: #2 alternative fragment length(s) may be 24,55,96,131,156,174,219,239,270,316,342,428,463,496,534 bps INFO @ Fri, 05 Jul 2019 17:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.05_model.r INFO @ Fri, 05 Jul 2019 17:41:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:41:59: 1000000 INFO @ Fri, 05 Jul 2019 17:41:59: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:41:59: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:41:59: #1 total tags in treatment: 520118 INFO @ Fri, 05 Jul 2019 17:41:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:41:59: #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 17:41:59: #1 tags after filtering in treatment: 441452 INFO @ Fri, 05 Jul 2019 17:41:59: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 17:41:59: #1 finished! INFO @ Fri, 05 Jul 2019 17:41:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:41:59: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 17:41:59: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 17:41:59: start model_add_line... INFO @ Fri, 05 Jul 2019 17:41:59: start X-correlation... INFO @ Fri, 05 Jul 2019 17:42:00: end of X-cor INFO @ Fri, 05 Jul 2019 17:42:00: #2 finished! INFO @ Fri, 05 Jul 2019 17:42:00: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 17:42:00: #2 alternative fragment length(s) may be 24,55,96,131,156,174,219,239,270,316,342,428,463,496,534 bps INFO @ Fri, 05 Jul 2019 17:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.10_model.r INFO @ Fri, 05 Jul 2019 17:42:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:42:00: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:42:00: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:42:00: #1 total tags in treatment: 520118 INFO @ Fri, 05 Jul 2019 17:42:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:42:00: #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 17:42:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:42:00: #1 tags after filtering in treatment: 441452 INFO @ Fri, 05 Jul 2019 17:42:00: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 17:42:00: #1 finished! INFO @ Fri, 05 Jul 2019 17:42:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:42:00: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 17:42:00: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 17:42:00: start model_add_line... INFO @ Fri, 05 Jul 2019 17:42:00: start X-correlation... INFO @ Fri, 05 Jul 2019 17:42:00: end of X-cor INFO @ Fri, 05 Jul 2019 17:42:00: #2 finished! INFO @ Fri, 05 Jul 2019 17:42:00: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 17:42:00: #2 alternative fragment length(s) may be 24,55,96,131,156,174,219,239,270,316,342,428,463,496,534 bps INFO @ Fri, 05 Jul 2019 17:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.20_model.r INFO @ Fri, 05 Jul 2019 17:42:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.05_summits.bed INFO @ Fri, 05 Jul 2019 17:42:01: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:42:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.10_summits.bed INFO @ Fri, 05 Jul 2019 17:42:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:42:02: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:42:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.20_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585702/ERX585702.20_summits.bed INFO @ Fri, 05 Jul 2019 17:42:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。