Job ID = 1300433 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:14:01 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-06-03T10:14:01 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-06-03T10:14:01 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 ) 2019-06-03T10:14:01 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 ) 2019-06-03T10:14:35 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 ) 2019-06-03T10:14:35 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 : 9,575,374 reads read : 9,575,374 reads written : 9,575,374 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: 00:03:23 9575374 reads; of these: 9575374 (100.00%) were unpaired; of these: 2120197 (22.14%) aligned 0 times 5066871 (52.92%) aligned exactly 1 time 2388306 (24.94%) aligned >1 times 77.86% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 397290 / 7455177 = 0.0533 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, 03 Jun 2019 19:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.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 @ Mon, 03 Jun 2019 19:20:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:20:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.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 @ Mon, 03 Jun 2019 19:20:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:20:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.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 @ Mon, 03 Jun 2019 19:20:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:20:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:21:03: 1000000 INFO @ Mon, 03 Jun 2019 19:21:03: 1000000 INFO @ Mon, 03 Jun 2019 19:21:04: 1000000 INFO @ Mon, 03 Jun 2019 19:21:11: 2000000 INFO @ Mon, 03 Jun 2019 19:21:12: 2000000 INFO @ Mon, 03 Jun 2019 19:21:13: 2000000 INFO @ Mon, 03 Jun 2019 19:21:20: 3000000 INFO @ Mon, 03 Jun 2019 19:21:22: 3000000 INFO @ Mon, 03 Jun 2019 19:21:23: 3000000 INFO @ Mon, 03 Jun 2019 19:21:29: 4000000 INFO @ Mon, 03 Jun 2019 19:21:30: 4000000 INFO @ Mon, 03 Jun 2019 19:21:32: 4000000 INFO @ Mon, 03 Jun 2019 19:21:37: 5000000 INFO @ Mon, 03 Jun 2019 19:21:40: 5000000 INFO @ Mon, 03 Jun 2019 19:21:41: 5000000 INFO @ Mon, 03 Jun 2019 19:21:46: 6000000 INFO @ Mon, 03 Jun 2019 19:21:49: 6000000 INFO @ Mon, 03 Jun 2019 19:21:51: 6000000 INFO @ Mon, 03 Jun 2019 19:21:54: 7000000 INFO @ Mon, 03 Jun 2019 19:21:55: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 19:21:55: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 19:21:55: #1 total tags in treatment: 7057887 INFO @ Mon, 03 Jun 2019 19:21:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:21:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:21:55: #1 tags after filtering in treatment: 7057887 INFO @ Mon, 03 Jun 2019 19:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:21:55: #1 finished! INFO @ Mon, 03 Jun 2019 19:21:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:21:56: #2 number of paired peaks: 379 WARNING @ Mon, 03 Jun 2019 19:21:56: 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, 03 Jun 2019 19:21:56: start model_add_line... INFO @ Mon, 03 Jun 2019 19:21:56: start X-correlation... INFO @ Mon, 03 Jun 2019 19:21:56: end of X-cor INFO @ Mon, 03 Jun 2019 19:21:56: #2 finished! INFO @ Mon, 03 Jun 2019 19:21:56: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 19:21:56: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 19:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.20_model.r WARNING @ Mon, 03 Jun 2019 19:21:56: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:21:56: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 19:21:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:21:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:21:58: 7000000 INFO @ Mon, 03 Jun 2019 19:21:59: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 19:21:59: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 19:21:59: #1 total tags in treatment: 7057887 INFO @ Mon, 03 Jun 2019 19:21:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:21:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:21:59: #1 tags after filtering in treatment: 7057887 INFO @ Mon, 03 Jun 2019 19:21:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:21:59: #1 finished! INFO @ Mon, 03 Jun 2019 19:21:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:21:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:22:00: #2 number of paired peaks: 379 WARNING @ Mon, 03 Jun 2019 19:22:00: 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, 03 Jun 2019 19:22:00: start model_add_line... INFO @ Mon, 03 Jun 2019 19:22:00: start X-correlation... INFO @ Mon, 03 Jun 2019 19:22:00: end of X-cor INFO @ Mon, 03 Jun 2019 19:22:00: #2 finished! INFO @ Mon, 03 Jun 2019 19:22:00: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 19:22:00: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 19:22:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.10_model.r WARNING @ Mon, 03 Jun 2019 19:22:00: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:22:00: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 19:22:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:22:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:22:00: 7000000 INFO @ Mon, 03 Jun 2019 19:22:01: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 19:22:01: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 19:22:01: #1 total tags in treatment: 7057887 INFO @ Mon, 03 Jun 2019 19:22:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:22:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:22:01: #1 tags after filtering in treatment: 7057887 INFO @ Mon, 03 Jun 2019 19:22:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:22:01: #1 finished! INFO @ Mon, 03 Jun 2019 19:22:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:22:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:22:02: #2 number of paired peaks: 379 WARNING @ Mon, 03 Jun 2019 19:22:02: 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, 03 Jun 2019 19:22:02: start model_add_line... INFO @ Mon, 03 Jun 2019 19:22:02: start X-correlation... INFO @ Mon, 03 Jun 2019 19:22:02: end of X-cor INFO @ Mon, 03 Jun 2019 19:22:02: #2 finished! INFO @ Mon, 03 Jun 2019 19:22:02: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 19:22:02: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 19:22:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.05_model.r WARNING @ Mon, 03 Jun 2019 19:22:02: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:22:02: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 19:22:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:22:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:22:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:22:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:22:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:22:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:22:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:22:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.20_summits.bed INFO @ Mon, 03 Jun 2019 19:22:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (783 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:22:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:22:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.10_summits.bed INFO @ Mon, 03 Jun 2019 19:22:33: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1279 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481128/SRX481128.05_summits.bed INFO @ Mon, 03 Jun 2019 19:22:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1690 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。