Job ID = 1292048 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T08:14:50 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 ) 2019-06-02T08:14:50 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 ) 2019-06-02T08:14:50 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 : 12,676,608 reads read : 12,676,608 reads written : 12,676,608 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:46 12676608 reads; of these: 12676608 (100.00%) were unpaired; of these: 1254935 (9.90%) aligned 0 times 9328956 (73.59%) aligned exactly 1 time 2092717 (16.51%) aligned >1 times 90.10% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7755889 / 11421673 = 0.6791 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 @ Sun, 02 Jun 2019 17:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.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 @ Sun, 02 Jun 2019 17:31:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.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 @ Sun, 02 Jun 2019 17:31:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.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 @ Sun, 02 Jun 2019 17:31:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:44: 1000000 INFO @ Sun, 02 Jun 2019 17:31:45: 1000000 INFO @ Sun, 02 Jun 2019 17:31:45: 1000000 INFO @ Sun, 02 Jun 2019 17:31:51: 2000000 INFO @ Sun, 02 Jun 2019 17:31:53: 2000000 INFO @ Sun, 02 Jun 2019 17:31:54: 2000000 INFO @ Sun, 02 Jun 2019 17:31:59: 3000000 INFO @ Sun, 02 Jun 2019 17:32:01: 3000000 INFO @ Sun, 02 Jun 2019 17:32:03: 3000000 INFO @ Sun, 02 Jun 2019 17:32:04: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 17:32:04: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 17:32:04: #1 total tags in treatment: 3665784 INFO @ Sun, 02 Jun 2019 17:32:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:32:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:32:04: #1 tags after filtering in treatment: 3665784 INFO @ Sun, 02 Jun 2019 17:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:32:04: #1 finished! INFO @ Sun, 02 Jun 2019 17:32:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:32:04: #2 number of paired peaks: 1212 INFO @ Sun, 02 Jun 2019 17:32:04: start model_add_line... INFO @ Sun, 02 Jun 2019 17:32:04: start X-correlation... INFO @ Sun, 02 Jun 2019 17:32:04: end of X-cor INFO @ Sun, 02 Jun 2019 17:32:04: #2 finished! INFO @ Sun, 02 Jun 2019 17:32:04: #2 predicted fragment length is 117 bps INFO @ Sun, 02 Jun 2019 17:32:04: #2 alternative fragment length(s) may be 117 bps INFO @ Sun, 02 Jun 2019 17:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.20_model.r WARNING @ Sun, 02 Jun 2019 17:32:04: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:32:04: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sun, 02 Jun 2019 17:32:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:32:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:32:06: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 17:32:06: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 17:32:06: #1 total tags in treatment: 3665784 INFO @ Sun, 02 Jun 2019 17:32:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:32:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:32:06: #1 tags after filtering in treatment: 3665784 INFO @ Sun, 02 Jun 2019 17:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:32:06: #1 finished! INFO @ Sun, 02 Jun 2019 17:32:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:32:07: #2 number of paired peaks: 1212 INFO @ Sun, 02 Jun 2019 17:32:07: start model_add_line... INFO @ Sun, 02 Jun 2019 17:32:07: start X-correlation... INFO @ Sun, 02 Jun 2019 17:32:07: end of X-cor INFO @ Sun, 02 Jun 2019 17:32:07: #2 finished! INFO @ Sun, 02 Jun 2019 17:32:07: #2 predicted fragment length is 117 bps INFO @ Sun, 02 Jun 2019 17:32:07: #2 alternative fragment length(s) may be 117 bps INFO @ Sun, 02 Jun 2019 17:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.10_model.r WARNING @ Sun, 02 Jun 2019 17:32:07: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:32:07: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sun, 02 Jun 2019 17:32:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:32:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:32:09: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 17:32:09: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 17:32:09: #1 total tags in treatment: 3665784 INFO @ Sun, 02 Jun 2019 17:32:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:32:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:32:09: #1 tags after filtering in treatment: 3665784 INFO @ Sun, 02 Jun 2019 17:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:32:09: #1 finished! INFO @ Sun, 02 Jun 2019 17:32:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:32:10: #2 number of paired peaks: 1212 INFO @ Sun, 02 Jun 2019 17:32:10: start model_add_line... INFO @ Sun, 02 Jun 2019 17:32:10: start X-correlation... INFO @ Sun, 02 Jun 2019 17:32:10: end of X-cor INFO @ Sun, 02 Jun 2019 17:32:10: #2 finished! INFO @ Sun, 02 Jun 2019 17:32:10: #2 predicted fragment length is 117 bps INFO @ Sun, 02 Jun 2019 17:32:10: #2 alternative fragment length(s) may be 117 bps INFO @ Sun, 02 Jun 2019 17:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.05_model.r WARNING @ Sun, 02 Jun 2019 17:32:10: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:32:10: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sun, 02 Jun 2019 17:32:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:32:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:32:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:32:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.20_summits.bed INFO @ Sun, 02 Jun 2019 17:32:22: Done! INFO @ Sun, 02 Jun 2019 17:32:22: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (885 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.10_summits.bed INFO @ Sun, 02 Jun 2019 17:32:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1451 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX330985/SRX330985.05_summits.bed INFO @ Sun, 02 Jun 2019 17:32:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2123 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。