Job ID = 2589963 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:52:00 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 ) 2019-08-12T09:52:23 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 ) 2019-08-12T09:52:23 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 : 5,349,280 reads read : 5,349,280 reads written : 5,349,280 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163560.sra.cache’: 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: 00:01:27 5349280 reads; of these: 5349280 (100.00%) were unpaired; of these: 721743 (13.49%) aligned 0 times 3822532 (71.46%) aligned exactly 1 time 805005 (15.05%) aligned >1 times 86.51% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 497910 / 4627537 = 0.1076 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 18:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.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 18:55:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:55:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.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 18:55:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:55:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.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 18:55:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:55:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:55:59: 1000000 INFO @ Mon, 12 Aug 2019 18:56:01: 1000000 INFO @ Mon, 12 Aug 2019 18:56:02: 1000000 INFO @ Mon, 12 Aug 2019 18:56:06: 2000000 INFO @ Mon, 12 Aug 2019 18:56:10: 2000000 INFO @ Mon, 12 Aug 2019 18:56:11: 2000000 INFO @ Mon, 12 Aug 2019 18:56:14: 3000000 INFO @ Mon, 12 Aug 2019 18:56:19: 3000000 INFO @ Mon, 12 Aug 2019 18:56:20: 3000000 INFO @ Mon, 12 Aug 2019 18:56:21: 4000000 INFO @ Mon, 12 Aug 2019 18:56:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:56:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:56:22: #1 total tags in treatment: 4129627 INFO @ Mon, 12 Aug 2019 18:56:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:56:22: #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 18:56:22: #1 tags after filtering in treatment: 4129627 INFO @ Mon, 12 Aug 2019 18:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:56:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:56:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:56:23: #2 number of paired peaks: 351 WARNING @ Mon, 12 Aug 2019 18:56:23: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 12 Aug 2019 18:56:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:56:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:56:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:56:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:56:23: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 18:56:23: #2 alternative fragment length(s) may be 48,557,588 bps INFO @ Mon, 12 Aug 2019 18:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.05_model.r WARNING @ Mon, 12 Aug 2019 18:56:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:56:23: #2 You may need to consider one of the other alternative d(s): 48,557,588 WARNING @ Mon, 12 Aug 2019 18:56:23: #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 18:56:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:56:28: 4000000 INFO @ Mon, 12 Aug 2019 18:56:29: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:56:29: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:56:29: #1 total tags in treatment: 4129627 INFO @ Mon, 12 Aug 2019 18:56:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:56:29: #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 18:56:29: 4000000 INFO @ Mon, 12 Aug 2019 18:56:29: #1 tags after filtering in treatment: 4129627 INFO @ Mon, 12 Aug 2019 18:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:56:29: #1 finished! INFO @ Mon, 12 Aug 2019 18:56:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:56:30: #2 number of paired peaks: 351 WARNING @ Mon, 12 Aug 2019 18:56:30: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 12 Aug 2019 18:56:30: start model_add_line... INFO @ Mon, 12 Aug 2019 18:56:30: start X-correlation... INFO @ Mon, 12 Aug 2019 18:56:30: end of X-cor INFO @ Mon, 12 Aug 2019 18:56:30: #2 finished! INFO @ Mon, 12 Aug 2019 18:56:30: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 18:56:30: #2 alternative fragment length(s) may be 48,557,588 bps INFO @ Mon, 12 Aug 2019 18:56:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.10_model.r WARNING @ Mon, 12 Aug 2019 18:56:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:56:30: #2 You may need to consider one of the other alternative d(s): 48,557,588 WARNING @ Mon, 12 Aug 2019 18:56:30: #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 18:56:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:56:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 18:56:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 18:56:30: #1 total tags in treatment: 4129627 INFO @ Mon, 12 Aug 2019 18:56:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:56:30: #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 18:56:31: #1 tags after filtering in treatment: 4129627 INFO @ Mon, 12 Aug 2019 18:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:56:31: #1 finished! INFO @ Mon, 12 Aug 2019 18:56:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:56:31: #2 number of paired peaks: 351 WARNING @ Mon, 12 Aug 2019 18:56:31: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 12 Aug 2019 18:56:31: start model_add_line... INFO @ Mon, 12 Aug 2019 18:56:31: start X-correlation... INFO @ Mon, 12 Aug 2019 18:56:31: end of X-cor INFO @ Mon, 12 Aug 2019 18:56:31: #2 finished! INFO @ Mon, 12 Aug 2019 18:56:31: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 18:56:31: #2 alternative fragment length(s) may be 48,557,588 bps INFO @ Mon, 12 Aug 2019 18:56:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.20_model.r WARNING @ Mon, 12 Aug 2019 18:56:31: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:56:31: #2 You may need to consider one of the other alternative d(s): 48,557,588 WARNING @ Mon, 12 Aug 2019 18:56:31: #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 18:56:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:56:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:56:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:56:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:56:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.05_summits.bed INFO @ Mon, 12 Aug 2019 18:56:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:56:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:56:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.10_summits.bed INFO @ Mon, 12 Aug 2019 18:56:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466494/SRX466494.20_summits.bed INFO @ Mon, 12 Aug 2019 18:56:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。