Job ID = 2589501 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,488,882 reads read : 2,488,882 reads written : 2,488,882 2019-08-12T08:50:50 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 ) 2019-08-12T08:50:50 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 ) 2019-08-12T08:50:50 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 : 4,693,546 reads read : 4,693,546 reads written : 4,693,546 spots read : 3,180,657 reads read : 3,180,657 reads written : 3,180,657 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: 00:00:51 10363085 reads; of these: 10363085 (100.00%) were unpaired; of these: 9554636 (92.20%) aligned 0 times 697581 (6.73%) aligned exactly 1 time 110868 (1.07%) aligned >1 times 7.80% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 25846 / 808449 = 0.0320 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 @ Mon, 12 Aug 2019 17:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:56:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:56:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:56:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:56:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:56:43: #1 total tags in treatment: 782603 INFO @ Mon, 12 Aug 2019 17:56:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:56:43: #1 tags after filtering in treatment: 782603 INFO @ Mon, 12 Aug 2019 17:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:56:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:56:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:43: #2 number of paired peaks: 268 WARNING @ Mon, 12 Aug 2019 17:56:43: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:43: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 17:56:43: #2 alternative fragment length(s) may be 30,82,107,174,291,377,458,517,534,570 bps INFO @ Mon, 12 Aug 2019 17:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.10_model.r WARNING @ Mon, 12 Aug 2019 17:56:43: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:43: #2 You may need to consider one of the other alternative d(s): 30,82,107,174,291,377,458,517,534,570 WARNING @ Mon, 12 Aug 2019 17:56:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:56:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:56:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:56:44: #1 total tags in treatment: 782603 INFO @ Mon, 12 Aug 2019 17:56:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:56:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:56:44: #1 tags after filtering in treatment: 782603 INFO @ Mon, 12 Aug 2019 17:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:56:44: #1 finished! INFO @ Mon, 12 Aug 2019 17:56:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:44: #2 number of paired peaks: 268 WARNING @ Mon, 12 Aug 2019 17:56:44: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:44: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 17:56:44: #2 alternative fragment length(s) may be 30,82,107,174,291,377,458,517,534,570 bps INFO @ Mon, 12 Aug 2019 17:56:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.05_model.r WARNING @ Mon, 12 Aug 2019 17:56:44: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:44: #2 You may need to consider one of the other alternative d(s): 30,82,107,174,291,377,458,517,534,570 WARNING @ Mon, 12 Aug 2019 17:56:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:56:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:46: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:56:46: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:56:46: #1 total tags in treatment: 782603 INFO @ Mon, 12 Aug 2019 17:56:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:56:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:56:46: #1 tags after filtering in treatment: 782603 INFO @ Mon, 12 Aug 2019 17:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:56:46: #1 finished! INFO @ Mon, 12 Aug 2019 17:56:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:46: #2 number of paired peaks: 268 WARNING @ Mon, 12 Aug 2019 17:56:46: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:46: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:46: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:46: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:46: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:46: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 17:56:46: #2 alternative fragment length(s) may be 30,82,107,174,291,377,458,517,534,570 bps INFO @ Mon, 12 Aug 2019 17:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.20_model.r WARNING @ Mon, 12 Aug 2019 17:56:46: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:46: #2 You may need to consider one of the other alternative d(s): 30,82,107,174,291,377,458,517,534,570 WARNING @ Mon, 12 Aug 2019 17:56:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:56:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.10_summits.bed INFO @ Mon, 12 Aug 2019 17:56:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.05_summits.bed INFO @ Mon, 12 Aug 2019 17:56:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:56:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX188620/SRX188620.20_summits.bed INFO @ Mon, 12 Aug 2019 17:56:50: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。