Job ID = 2007909 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:39:12 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 ) 2019-07-05T07:40:38 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:38 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' spots read : 1,712,270 reads read : 3,424,540 reads written : 3,424,540 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: 00:02:02 1712270 reads; of these: 1712270 (100.00%) were paired; of these: 137150 (8.01%) aligned concordantly 0 times 1439111 (84.05%) aligned concordantly exactly 1 time 136009 (7.94%) aligned concordantly >1 times ---- 137150 pairs aligned concordantly 0 times; of these: 36708 (26.76%) aligned discordantly 1 time ---- 100442 pairs aligned 0 times concordantly or discordantly; of these: 200884 mates make up the pairs; of these: 173316 (86.28%) aligned 0 times 17452 (8.69%) aligned exactly 1 time 10116 (5.04%) aligned >1 times 94.94% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 89556 / 1601655 = 0.0559 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 16:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.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 16:47:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:47:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.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 16:47:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:47:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.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 16:47:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:47:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:47:18: 1000000 INFO @ Fri, 05 Jul 2019 16:47:20: 1000000 INFO @ Fri, 05 Jul 2019 16:47:21: 1000000 INFO @ Fri, 05 Jul 2019 16:47:27: 2000000 INFO @ Fri, 05 Jul 2019 16:47:31: 2000000 INFO @ Fri, 05 Jul 2019 16:47:32: 2000000 INFO @ Fri, 05 Jul 2019 16:47:38: 3000000 INFO @ Fri, 05 Jul 2019 16:47:39: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:47:39: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:47:39: #1 total tags in treatment: 1486377 INFO @ Fri, 05 Jul 2019 16:47:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:47:39: #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 16:47:39: #1 tags after filtering in treatment: 1414357 INFO @ Fri, 05 Jul 2019 16:47:39: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:47:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:47:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:47:39: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 16:47:39: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 16:47:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:47:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:47:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:47:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:47:39: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 16:47:39: #2 alternative fragment length(s) may be 15,22,46,80,101,128,154,192,217,230,259,302,348,382,401,436,454,483,521,546,574 bps INFO @ Fri, 05 Jul 2019 16:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.05_model.r WARNING @ Fri, 05 Jul 2019 16:47:39: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:47:39: #2 You may need to consider one of the other alternative d(s): 15,22,46,80,101,128,154,192,217,230,259,302,348,382,401,436,454,483,521,546,574 WARNING @ Fri, 05 Jul 2019 16:47:39: #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 16:47:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:47:41: 3000000 INFO @ Fri, 05 Jul 2019 16:47:42: 3000000 INFO @ Fri, 05 Jul 2019 16:47:42: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:47:42: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:47:42: #1 total tags in treatment: 1486377 INFO @ Fri, 05 Jul 2019 16:47:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:47:42: #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 16:47:42: #1 tags after filtering in treatment: 1414357 INFO @ Fri, 05 Jul 2019 16:47:42: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:47:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:47:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:47:42: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 16:47:42: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 16:47:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:47:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:47:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:47:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:47:42: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 16:47:42: #2 alternative fragment length(s) may be 15,22,46,80,101,128,154,192,217,230,259,302,348,382,401,436,454,483,521,546,574 bps INFO @ Fri, 05 Jul 2019 16:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.20_model.r WARNING @ Fri, 05 Jul 2019 16:47:42: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:47:42: #2 You may need to consider one of the other alternative d(s): 15,22,46,80,101,128,154,192,217,230,259,302,348,382,401,436,454,483,521,546,574 WARNING @ Fri, 05 Jul 2019 16:47:42: #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 16:47:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:47:42: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:47:42: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:47:42: #1 total tags in treatment: 1486377 INFO @ Fri, 05 Jul 2019 16:47:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:47:42: #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 16:47:42: #1 tags after filtering in treatment: 1414357 INFO @ Fri, 05 Jul 2019 16:47:42: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:47:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:47:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:47:42: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 16:47:42: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 16:47:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:47:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:47:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:47:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:47:43: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 16:47:43: #2 alternative fragment length(s) may be 15,22,46,80,101,128,154,192,217,230,259,302,348,382,401,436,454,483,521,546,574 bps INFO @ Fri, 05 Jul 2019 16:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.10_model.r WARNING @ Fri, 05 Jul 2019 16:47:43: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:47:43: #2 You may need to consider one of the other alternative d(s): 15,22,46,80,101,128,154,192,217,230,259,302,348,382,401,436,454,483,521,546,574 WARNING @ Fri, 05 Jul 2019 16:47:43: #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 16:47:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:47:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.05_summits.bed INFO @ Fri, 05 Jul 2019 16:47:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:47:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:47:47: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.20_summits.bed INFO @ Fri, 05 Jul 2019 16:47:48: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471708/ERX471708.10_summits.bed INFO @ Fri, 05 Jul 2019 16:47:49: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。