Job ID = 2008172 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:31:35 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 528,604 reads read : 1,057,208 reads written : 1,057,208 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628964.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: 00:00:28 528604 reads; of these: 528604 (100.00%) were paired; of these: 18069 (3.42%) aligned concordantly 0 times 453551 (85.80%) aligned concordantly exactly 1 time 56984 (10.78%) aligned concordantly >1 times ---- 18069 pairs aligned concordantly 0 times; of these: 7151 (39.58%) aligned discordantly 1 time ---- 10918 pairs aligned 0 times concordantly or discordantly; of these: 21836 mates make up the pairs; of these: 11896 (54.48%) aligned 0 times 3480 (15.94%) aligned exactly 1 time 6460 (29.58%) aligned >1 times 98.87% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 183302 / 515724 = 0.3554 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 17:32:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.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 17:32:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.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 17:32:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.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 17:32:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:33:02: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:33:02: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:33:02: #1 total tags in treatment: 328071 INFO @ Fri, 05 Jul 2019 17:33:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:02: #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 17:33:02: #1 tags after filtering in treatment: 295017 INFO @ Fri, 05 Jul 2019 17:33:02: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 17:33:02: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:02: #2 number of paired peaks: 104 WARNING @ Fri, 05 Jul 2019 17:33:02: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:02: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:02: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:02: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:02: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:02: #2 predicted fragment length is 86 bps INFO @ Fri, 05 Jul 2019 17:33:02: #2 alternative fragment length(s) may be 86,196,227,291,444,466,497 bps INFO @ Fri, 05 Jul 2019 17:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.05_model.r WARNING @ Fri, 05 Jul 2019 17:33:02: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:33:02: #2 You may need to consider one of the other alternative d(s): 86,196,227,291,444,466,497 WARNING @ Fri, 05 Jul 2019 17:33:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:33:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:03: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:33:03: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:33:03: #1 total tags in treatment: 328071 INFO @ Fri, 05 Jul 2019 17:33:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:03: #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 17:33:03: #1 tags after filtering in treatment: 295017 INFO @ Fri, 05 Jul 2019 17:33:03: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 17:33:03: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:03: #2 number of paired peaks: 104 WARNING @ Fri, 05 Jul 2019 17:33:03: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:03: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:03: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:03: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:03: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:03: #2 predicted fragment length is 86 bps INFO @ Fri, 05 Jul 2019 17:33:03: #2 alternative fragment length(s) may be 86,196,227,291,444,466,497 bps INFO @ Fri, 05 Jul 2019 17:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.10_model.r WARNING @ Fri, 05 Jul 2019 17:33:03: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:33:03: #2 You may need to consider one of the other alternative d(s): 86,196,227,291,444,466,497 WARNING @ Fri, 05 Jul 2019 17:33:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:33:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.05_summits.bed INFO @ Fri, 05 Jul 2019 17:33:03: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:33:03: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:33:03: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:33:03: #1 total tags in treatment: 328071 INFO @ Fri, 05 Jul 2019 17:33:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:03: #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 17:33:04: #1 tags after filtering in treatment: 295017 INFO @ Fri, 05 Jul 2019 17:33:04: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 17:33:04: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:04: #2 number of paired peaks: 104 WARNING @ Fri, 05 Jul 2019 17:33:04: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:04: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:04: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:04: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:04: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:04: #2 predicted fragment length is 86 bps INFO @ Fri, 05 Jul 2019 17:33:04: #2 alternative fragment length(s) may be 86,196,227,291,444,466,497 bps INFO @ Fri, 05 Jul 2019 17:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.20_model.r WARNING @ Fri, 05 Jul 2019 17:33:04: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:33:04: #2 You may need to consider one of the other alternative d(s): 86,196,227,291,444,466,497 WARNING @ Fri, 05 Jul 2019 17:33:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:33:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.10_summits.bed INFO @ Fri, 05 Jul 2019 17:33:04: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:33:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585709/ERX585709.20_summits.bed INFO @ Fri, 05 Jul 2019 17:33:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。