Job ID = 3785877 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:36:40 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 ) 2019-11-01T05:37:48 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 ) 2019-11-01T05:39:46 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 : 5,839,095 reads read : 11,678,190 reads written : 5,839,095 reads 0-length : 5,839,095 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: 00:01:02 5839095 reads; of these: 5839095 (100.00%) were unpaired; of these: 5722373 (98.00%) aligned 0 times 8659 (0.15%) aligned exactly 1 time 108063 (1.85%) aligned >1 times 2.00% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 99356 / 116722 = 0.8512 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 01 Nov 2019 14:42:51: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:42:51: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:42:51: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:42:51: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:42:51: #1 total tags in treatment: 17366 INFO @ Fri, 01 Nov 2019 14:42:51: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:42:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:42:51: #1 tags after filtering in treatment: 17366 INFO @ Fri, 01 Nov 2019 14:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:42:51: #1 finished! INFO @ Fri, 01 Nov 2019 14:42:51: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:42:51: #2 number of paired peaks: 300 WARNING @ Fri, 01 Nov 2019 14:42:51: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 01 Nov 2019 14:42:51: start model_add_line... INFO @ Fri, 01 Nov 2019 14:42:51: start X-correlation... INFO @ Fri, 01 Nov 2019 14:42:51: end of X-cor INFO @ Fri, 01 Nov 2019 14:42:51: #2 finished! INFO @ Fri, 01 Nov 2019 14:42:51: #2 predicted fragment length is 74 bps INFO @ Fri, 01 Nov 2019 14:42:51: #2 alternative fragment length(s) may be 74,102,129,212,232,262,285,569,589 bps INFO @ Fri, 01 Nov 2019 14:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.05_model.r WARNING @ Fri, 01 Nov 2019 14:42:51: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:42:51: #2 You may need to consider one of the other alternative d(s): 74,102,129,212,232,262,285,569,589 WARNING @ Fri, 01 Nov 2019 14:42:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:42:51: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:42:51: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.05_summits.bed INFO @ Fri, 01 Nov 2019 14:42:51: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (92 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 01 Nov 2019 14:43:21: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:43:21: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:43:21: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:43:21: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:43:21: #1 total tags in treatment: 17366 INFO @ Fri, 01 Nov 2019 14:43:21: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:43:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:43:21: #1 tags after filtering in treatment: 17366 INFO @ Fri, 01 Nov 2019 14:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:43:21: #1 finished! INFO @ Fri, 01 Nov 2019 14:43:21: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:43:21: #2 number of paired peaks: 300 WARNING @ Fri, 01 Nov 2019 14:43:21: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 01 Nov 2019 14:43:21: start model_add_line... INFO @ Fri, 01 Nov 2019 14:43:21: start X-correlation... INFO @ Fri, 01 Nov 2019 14:43:21: end of X-cor INFO @ Fri, 01 Nov 2019 14:43:21: #2 finished! INFO @ Fri, 01 Nov 2019 14:43:21: #2 predicted fragment length is 74 bps INFO @ Fri, 01 Nov 2019 14:43:21: #2 alternative fragment length(s) may be 74,102,129,212,232,262,285,569,589 bps INFO @ Fri, 01 Nov 2019 14:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.10_model.r WARNING @ Fri, 01 Nov 2019 14:43:21: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:43:21: #2 You may need to consider one of the other alternative d(s): 74,102,129,212,232,262,285,569,589 WARNING @ Fri, 01 Nov 2019 14:43:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:43:21: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:43:21: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.10_summits.bed INFO @ Fri, 01 Nov 2019 14:43:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 01 Nov 2019 14:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 01 Nov 2019 14:43:51: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:43:51: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:43:51: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:43:51: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:43:51: #1 total tags in treatment: 17366 INFO @ Fri, 01 Nov 2019 14:43:51: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:43:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:43:51: #1 tags after filtering in treatment: 17366 INFO @ Fri, 01 Nov 2019 14:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:43:51: #1 finished! INFO @ Fri, 01 Nov 2019 14:43:51: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:43:51: #2 number of paired peaks: 300 WARNING @ Fri, 01 Nov 2019 14:43:51: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 01 Nov 2019 14:43:51: start model_add_line... INFO @ Fri, 01 Nov 2019 14:43:51: start X-correlation... INFO @ Fri, 01 Nov 2019 14:43:51: end of X-cor INFO @ Fri, 01 Nov 2019 14:43:51: #2 finished! INFO @ Fri, 01 Nov 2019 14:43:51: #2 predicted fragment length is 74 bps INFO @ Fri, 01 Nov 2019 14:43:51: #2 alternative fragment length(s) may be 74,102,129,212,232,262,285,569,589 bps INFO @ Fri, 01 Nov 2019 14:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.20_model.r WARNING @ Fri, 01 Nov 2019 14:43:51: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:43:51: #2 You may need to consider one of the other alternative d(s): 74,102,129,212,232,262,285,569,589 WARNING @ Fri, 01 Nov 2019 14:43:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:43:51: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:43:52: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426114/SRX5426114.20_summits.bed INFO @ Fri, 01 Nov 2019 14:43:52: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling