Job ID = 2590171 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:53:27 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 ) 2019-08-12T10:53:27 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 ) 2019-08-12T10:53:27 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 ) 2019-08-12T10:53:27 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 : 27,236,726 reads read : 27,236,726 reads written : 27,236,726 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: 00:06:23 27236726 reads; of these: 27236726 (100.00%) were unpaired; of these: 3797566 (13.94%) aligned 0 times 20850573 (76.55%) aligned exactly 1 time 2588587 (9.50%) aligned >1 times 86.06% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12246933 / 23439160 = 0.5225 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 20:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.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 20:18:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:18:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.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 20:18:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:18:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.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 20:18:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:18:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:18:22: 1000000 INFO @ Mon, 12 Aug 2019 20:18:23: 1000000 INFO @ Mon, 12 Aug 2019 20:18:24: 1000000 INFO @ Mon, 12 Aug 2019 20:18:29: 2000000 INFO @ Mon, 12 Aug 2019 20:18:30: 2000000 INFO @ Mon, 12 Aug 2019 20:18:31: 2000000 INFO @ Mon, 12 Aug 2019 20:18:36: 3000000 INFO @ Mon, 12 Aug 2019 20:18:37: 3000000 INFO @ Mon, 12 Aug 2019 20:18:38: 3000000 INFO @ Mon, 12 Aug 2019 20:18:44: 4000000 INFO @ Mon, 12 Aug 2019 20:18:45: 4000000 INFO @ Mon, 12 Aug 2019 20:18:46: 4000000 INFO @ Mon, 12 Aug 2019 20:18:51: 5000000 INFO @ Mon, 12 Aug 2019 20:18:52: 5000000 INFO @ Mon, 12 Aug 2019 20:18:53: 5000000 INFO @ Mon, 12 Aug 2019 20:18:58: 6000000 INFO @ Mon, 12 Aug 2019 20:18:59: 6000000 INFO @ Mon, 12 Aug 2019 20:19:01: 6000000 INFO @ Mon, 12 Aug 2019 20:19:06: 7000000 INFO @ Mon, 12 Aug 2019 20:19:07: 7000000 INFO @ Mon, 12 Aug 2019 20:19:09: 7000000 INFO @ Mon, 12 Aug 2019 20:19:13: 8000000 INFO @ Mon, 12 Aug 2019 20:19:14: 8000000 INFO @ Mon, 12 Aug 2019 20:19:16: 8000000 INFO @ Mon, 12 Aug 2019 20:19:21: 9000000 INFO @ Mon, 12 Aug 2019 20:19:21: 9000000 INFO @ Mon, 12 Aug 2019 20:19:25: 9000000 INFO @ Mon, 12 Aug 2019 20:19:28: 10000000 INFO @ Mon, 12 Aug 2019 20:19:29: 10000000 INFO @ Mon, 12 Aug 2019 20:19:32: 10000000 INFO @ Mon, 12 Aug 2019 20:19:36: 11000000 INFO @ Mon, 12 Aug 2019 20:19:36: 11000000 INFO @ Mon, 12 Aug 2019 20:19:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:19:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:19:37: #1 total tags in treatment: 11192227 INFO @ Mon, 12 Aug 2019 20:19:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:19:37: #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 20:19:37: #1 tags after filtering in treatment: 11192227 INFO @ Mon, 12 Aug 2019 20:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:19:37: #1 finished! INFO @ Mon, 12 Aug 2019 20:19:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:19:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:19:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:19:38: #1 total tags in treatment: 11192227 INFO @ Mon, 12 Aug 2019 20:19:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:19:38: #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 20:19:38: #1 tags after filtering in treatment: 11192227 INFO @ Mon, 12 Aug 2019 20:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:19:38: #1 finished! INFO @ Mon, 12 Aug 2019 20:19:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:19:39: #2 number of paired peaks: 990 WARNING @ Mon, 12 Aug 2019 20:19:39: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Mon, 12 Aug 2019 20:19:39: start model_add_line... INFO @ Mon, 12 Aug 2019 20:19:39: start X-correlation... INFO @ Mon, 12 Aug 2019 20:19:39: end of X-cor INFO @ Mon, 12 Aug 2019 20:19:39: #2 finished! INFO @ Mon, 12 Aug 2019 20:19:39: #2 predicted fragment length is 131 bps INFO @ Mon, 12 Aug 2019 20:19:39: #2 alternative fragment length(s) may be 3,110,131,150 bps INFO @ Mon, 12 Aug 2019 20:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.05_model.r INFO @ Mon, 12 Aug 2019 20:19:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:19:39: #2 number of paired peaks: 990 WARNING @ Mon, 12 Aug 2019 20:19:39: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Mon, 12 Aug 2019 20:19:39: start model_add_line... INFO @ Mon, 12 Aug 2019 20:19:39: start X-correlation... INFO @ Mon, 12 Aug 2019 20:19:39: end of X-cor INFO @ Mon, 12 Aug 2019 20:19:39: #2 finished! INFO @ Mon, 12 Aug 2019 20:19:39: #2 predicted fragment length is 131 bps INFO @ Mon, 12 Aug 2019 20:19:39: #2 alternative fragment length(s) may be 3,110,131,150 bps INFO @ Mon, 12 Aug 2019 20:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.10_model.r INFO @ Mon, 12 Aug 2019 20:19:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:19:40: 11000000 INFO @ Mon, 12 Aug 2019 20:19:42: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:19:42: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:19:42: #1 total tags in treatment: 11192227 INFO @ Mon, 12 Aug 2019 20:19:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:19:42: #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 20:19:42: #1 tags after filtering in treatment: 11192227 INFO @ Mon, 12 Aug 2019 20:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:19:42: #1 finished! INFO @ Mon, 12 Aug 2019 20:19:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:19:43: #2 number of paired peaks: 990 WARNING @ Mon, 12 Aug 2019 20:19:43: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Mon, 12 Aug 2019 20:19:43: start model_add_line... INFO @ Mon, 12 Aug 2019 20:19:43: start X-correlation... INFO @ Mon, 12 Aug 2019 20:19:43: end of X-cor INFO @ Mon, 12 Aug 2019 20:19:43: #2 finished! INFO @ Mon, 12 Aug 2019 20:19:43: #2 predicted fragment length is 131 bps INFO @ Mon, 12 Aug 2019 20:19:43: #2 alternative fragment length(s) may be 3,110,131,150 bps INFO @ Mon, 12 Aug 2019 20:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.20_model.r INFO @ Mon, 12 Aug 2019 20:19:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:20:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:20:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:20:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:20:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:20:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.05_summits.bed INFO @ Mon, 12 Aug 2019 20:20:25: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (7630 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:20:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:20:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.10_summits.bed INFO @ Mon, 12 Aug 2019 20:20:25: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2609 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495044/SRX495044.20_summits.bed INFO @ Mon, 12 Aug 2019 20:20:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。