Job ID = 2010024 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T11:57:25 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 ) 2019-07-05T11:57:25 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 ) 2019-07-05T11:57:25 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 : 5,733,359 reads read : 11,466,718 reads written : 5,733,359 reads 0-length : 5,733,359 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: 00:01:43 5733359 reads; of these: 5733359 (100.00%) were unpaired; of these: 488057 (8.51%) aligned 0 times 3095641 (53.99%) aligned exactly 1 time 2149661 (37.49%) aligned >1 times 91.49% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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_rmdupse_core] 3266888 / 5245302 = 0.6228 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 21:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.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 21:01:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:01:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.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 21:01:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:01:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.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 21:01:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:01:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:01:49: 1000000 INFO @ Fri, 05 Jul 2019 21:01:50: 1000000 INFO @ Fri, 05 Jul 2019 21:01:51: 1000000 INFO @ Fri, 05 Jul 2019 21:01:58: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:01:58: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:01:58: #1 total tags in treatment: 1978414 INFO @ Fri, 05 Jul 2019 21:01:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:01:58: #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 21:01:58: #1 tags after filtering in treatment: 1978414 INFO @ Fri, 05 Jul 2019 21:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:01:58: #1 finished! INFO @ Fri, 05 Jul 2019 21:01:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:01:58: #2 number of paired peaks: 170 WARNING @ Fri, 05 Jul 2019 21:01:58: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 05 Jul 2019 21:01:58: start model_add_line... INFO @ Fri, 05 Jul 2019 21:01:58: start X-correlation... INFO @ Fri, 05 Jul 2019 21:01:58: end of X-cor INFO @ Fri, 05 Jul 2019 21:01:58: #2 finished! INFO @ Fri, 05 Jul 2019 21:01:58: #2 predicted fragment length is 88 bps INFO @ Fri, 05 Jul 2019 21:01:58: #2 alternative fragment length(s) may be 3,88,103 bps INFO @ Fri, 05 Jul 2019 21:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.20_model.r WARNING @ Fri, 05 Jul 2019 21:01:58: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:01:58: #2 You may need to consider one of the other alternative d(s): 3,88,103 WARNING @ Fri, 05 Jul 2019 21:01:58: #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 21:01:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:01:59: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:01:59: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:01:59: #1 total tags in treatment: 1978414 INFO @ Fri, 05 Jul 2019 21:01:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:01:59: #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 21:01:59: #1 tags after filtering in treatment: 1978414 INFO @ Fri, 05 Jul 2019 21:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:01:59: #1 finished! INFO @ Fri, 05 Jul 2019 21:01:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:01:59: #2 number of paired peaks: 170 WARNING @ Fri, 05 Jul 2019 21:01:59: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 05 Jul 2019 21:01:59: start model_add_line... INFO @ Fri, 05 Jul 2019 21:01:59: start X-correlation... INFO @ Fri, 05 Jul 2019 21:01:59: end of X-cor INFO @ Fri, 05 Jul 2019 21:01:59: #2 finished! INFO @ Fri, 05 Jul 2019 21:01:59: #2 predicted fragment length is 88 bps INFO @ Fri, 05 Jul 2019 21:01:59: #2 alternative fragment length(s) may be 3,88,103 bps INFO @ Fri, 05 Jul 2019 21:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.05_model.r WARNING @ Fri, 05 Jul 2019 21:01:59: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:01:59: #2 You may need to consider one of the other alternative d(s): 3,88,103 WARNING @ Fri, 05 Jul 2019 21:01:59: #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 21:01:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:02:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:00: #1 total tags in treatment: 1978414 INFO @ Fri, 05 Jul 2019 21:02:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:00: #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 21:02:00: #1 tags after filtering in treatment: 1978414 INFO @ Fri, 05 Jul 2019 21:02:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:02:00: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:00: #2 number of paired peaks: 170 WARNING @ Fri, 05 Jul 2019 21:02:00: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 05 Jul 2019 21:02:00: start model_add_line... INFO @ Fri, 05 Jul 2019 21:02:00: start X-correlation... INFO @ Fri, 05 Jul 2019 21:02:00: end of X-cor INFO @ Fri, 05 Jul 2019 21:02:00: #2 finished! INFO @ Fri, 05 Jul 2019 21:02:00: #2 predicted fragment length is 88 bps INFO @ Fri, 05 Jul 2019 21:02:00: #2 alternative fragment length(s) may be 3,88,103 bps INFO @ Fri, 05 Jul 2019 21:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.10_model.r WARNING @ Fri, 05 Jul 2019 21:02:00: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:02:00: #2 You may need to consider one of the other alternative d(s): 3,88,103 WARNING @ Fri, 05 Jul 2019 21:02:00: #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 21:02:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:02:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:02:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:02:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.20_summits.bed INFO @ Fri, 05 Jul 2019 21:02:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 21:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.05_summits.bed INFO @ Fri, 05 Jul 2019 21:02:07: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (260 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX249056/SRX249056.10_summits.bed INFO @ Fri, 05 Jul 2019 21:02:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (161 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。