Job ID = 2589953 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:49:29 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault 2019-08-12T09:51:31 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 ) 2019-08-12T09:51:32 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 : 8,667,423 reads read : 8,667,423 reads written : 8,667,423 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: 00:02:35 8667423 reads; of these: 8667423 (100.00%) were unpaired; of these: 153228 (1.77%) aligned 0 times 7020800 (81.00%) aligned exactly 1 time 1493395 (17.23%) aligned >1 times 98.23% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 809102 / 8514195 = 0.0950 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 19:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.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 19:00:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.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 19:00:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.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 19:00:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:32: 1000000 INFO @ Mon, 12 Aug 2019 19:00:34: 1000000 INFO @ Mon, 12 Aug 2019 19:00:35: 1000000 INFO @ Mon, 12 Aug 2019 19:00:40: 2000000 INFO @ Mon, 12 Aug 2019 19:00:41: 2000000 INFO @ Mon, 12 Aug 2019 19:00:43: 2000000 INFO @ Mon, 12 Aug 2019 19:00:48: 3000000 INFO @ Mon, 12 Aug 2019 19:00:48: 3000000 INFO @ Mon, 12 Aug 2019 19:00:52: 3000000 INFO @ Mon, 12 Aug 2019 19:00:55: 4000000 INFO @ Mon, 12 Aug 2019 19:00:55: 4000000 INFO @ Mon, 12 Aug 2019 19:01:01: 4000000 INFO @ Mon, 12 Aug 2019 19:01:02: 5000000 INFO @ Mon, 12 Aug 2019 19:01:03: 5000000 INFO @ Mon, 12 Aug 2019 19:01:09: 6000000 INFO @ Mon, 12 Aug 2019 19:01:09: 5000000 INFO @ Mon, 12 Aug 2019 19:01:10: 6000000 INFO @ Mon, 12 Aug 2019 19:01:15: 7000000 INFO @ Mon, 12 Aug 2019 19:01:18: 6000000 INFO @ Mon, 12 Aug 2019 19:01:18: 7000000 INFO @ Mon, 12 Aug 2019 19:01:20: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:20: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:20: #1 total tags in treatment: 7705093 INFO @ Mon, 12 Aug 2019 19:01:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:20: #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 19:01:20: #1 tags after filtering in treatment: 7705093 INFO @ Mon, 12 Aug 2019 19:01:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:20: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:21: #2 number of paired peaks: 379 WARNING @ Mon, 12 Aug 2019 19:01:21: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:21: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:21: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:21: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:21: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:21: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:01:21: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 12 Aug 2019 19:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.20_model.r WARNING @ Mon, 12 Aug 2019 19:01:21: #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 19:01:21: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 12 Aug 2019 19:01:21: #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 19:01:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:23: #1 total tags in treatment: 7705093 INFO @ Mon, 12 Aug 2019 19:01:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:23: #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 19:01:23: #1 tags after filtering in treatment: 7705093 INFO @ Mon, 12 Aug 2019 19:01:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:23: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:24: #2 number of paired peaks: 379 WARNING @ Mon, 12 Aug 2019 19:01:24: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:24: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:24: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:24: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:24: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:24: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:01:24: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 12 Aug 2019 19:01:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.05_model.r WARNING @ Mon, 12 Aug 2019 19:01:24: #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 19:01:24: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 12 Aug 2019 19:01:24: #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 19:01:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:26: 7000000 INFO @ Mon, 12 Aug 2019 19:01:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:32: #1 total tags in treatment: 7705093 INFO @ Mon, 12 Aug 2019 19:01:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:32: #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 19:01:32: #1 tags after filtering in treatment: 7705093 INFO @ Mon, 12 Aug 2019 19:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:32: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:33: #2 number of paired peaks: 379 WARNING @ Mon, 12 Aug 2019 19:01:33: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:33: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:33: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:33: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:33: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:33: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:01:33: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 12 Aug 2019 19:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.10_model.r WARNING @ Mon, 12 Aug 2019 19:01:33: #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 19:01:33: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 12 Aug 2019 19:01:33: #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 19:01:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.20_summits.bed INFO @ Mon, 12 Aug 2019 19:01:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:01:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.05_summits.bed INFO @ Mon, 12 Aug 2019 19:01:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (625 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466484/SRX466484.10_summits.bed INFO @ Mon, 12 Aug 2019 19:02:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。