Job ID = 2640431 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:43:28 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 : 117,231,717 reads read : 117,231,717 reads written : 117,231,717 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR980347.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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:52:04 117231717 reads; of these: 117231717 (100.00%) were unpaired; of these: 28462397 (24.28%) aligned 0 times 69403083 (59.20%) aligned exactly 1 time 19366237 (16.52%) aligned >1 times 75.72% overall alignment rate Time searching: 01:52:07 Overall time: 01:52:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 40 files... [bam_rmdupse_core] 75498322 / 88769320 = 0.8505 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:58:51: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:58:51: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:00: 1000000 INFO @ Sat, 24 Aug 2019 18:59:08: 2000000 INFO @ Sat, 24 Aug 2019 18:59:16: 3000000 INFO @ Sat, 24 Aug 2019 18:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:59:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:59:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:25: 4000000 INFO @ Sat, 24 Aug 2019 18:59:28: 1000000 INFO @ Sat, 24 Aug 2019 18:59:33: 5000000 INFO @ Sat, 24 Aug 2019 18:59:37: 2000000 INFO @ Sat, 24 Aug 2019 18:59:42: 6000000 INFO @ Sat, 24 Aug 2019 18:59:44: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:59:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:59:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:59:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:51: 7000000 INFO @ Sat, 24 Aug 2019 18:59:52: 4000000 INFO @ Sat, 24 Aug 2019 19:00:00: 8000000 INFO @ Sat, 24 Aug 2019 19:00:00: 5000000 INFO @ Sat, 24 Aug 2019 19:00:00: 1000000 INFO @ Sat, 24 Aug 2019 19:00:07: 6000000 INFO @ Sat, 24 Aug 2019 19:00:09: 2000000 INFO @ Sat, 24 Aug 2019 19:00:09: 9000000 INFO @ Sat, 24 Aug 2019 19:00:15: 7000000 INFO @ Sat, 24 Aug 2019 19:00:17: 10000000 INFO @ Sat, 24 Aug 2019 19:00:18: 3000000 INFO @ Sat, 24 Aug 2019 19:00:22: 8000000 INFO @ Sat, 24 Aug 2019 19:00:26: 11000000 INFO @ Sat, 24 Aug 2019 19:00:27: 4000000 INFO @ Sat, 24 Aug 2019 19:00:29: 9000000 INFO @ Sat, 24 Aug 2019 19:00:35: 12000000 INFO @ Sat, 24 Aug 2019 19:00:35: 5000000 INFO @ Sat, 24 Aug 2019 19:00:36: 10000000 INFO @ Sat, 24 Aug 2019 19:00:43: 11000000 INFO @ Sat, 24 Aug 2019 19:00:44: 6000000 INFO @ Sat, 24 Aug 2019 19:00:44: 13000000 INFO @ Sat, 24 Aug 2019 19:00:46: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:00:46: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:00:46: #1 total tags in treatment: 13270998 INFO @ Sat, 24 Aug 2019 19:00:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:00:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:00:47: #1 tags after filtering in treatment: 13270869 INFO @ Sat, 24 Aug 2019 19:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:00:47: #1 finished! INFO @ Sat, 24 Aug 2019 19:00:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:00:50: #2 number of paired peaks: 32505 INFO @ Sat, 24 Aug 2019 19:00:50: start model_add_line... INFO @ Sat, 24 Aug 2019 19:00:50: start X-correlation... INFO @ Sat, 24 Aug 2019 19:00:50: end of X-cor INFO @ Sat, 24 Aug 2019 19:00:50: #2 finished! INFO @ Sat, 24 Aug 2019 19:00:50: #2 predicted fragment length is 81 bps INFO @ Sat, 24 Aug 2019 19:00:50: #2 alternative fragment length(s) may be 81,302,462,542 bps INFO @ Sat, 24 Aug 2019 19:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.05_model.r WARNING @ Sat, 24 Aug 2019 19:00:50: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:00:50: #2 You may need to consider one of the other alternative d(s): 81,302,462,542 WARNING @ Sat, 24 Aug 2019 19:00:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:00:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:00:50: 12000000 INFO @ Sat, 24 Aug 2019 19:00:52: 7000000 INFO @ Sat, 24 Aug 2019 19:00:58: 13000000 INFO @ Sat, 24 Aug 2019 19:01:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:01:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:01:00: #1 total tags in treatment: 13270998 INFO @ Sat, 24 Aug 2019 19:01:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:01:00: #1 tags after filtering in treatment: 13270869 INFO @ Sat, 24 Aug 2019 19:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:00: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:01: 8000000 INFO @ Sat, 24 Aug 2019 19:01:04: #2 number of paired peaks: 32505 INFO @ Sat, 24 Aug 2019 19:01:04: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:04: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:04: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:04: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:04: #2 predicted fragment length is 81 bps INFO @ Sat, 24 Aug 2019 19:01:04: #2 alternative fragment length(s) may be 81,302,462,542 bps INFO @ Sat, 24 Aug 2019 19:01:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.10_model.r WARNING @ Sat, 24 Aug 2019 19:01:04: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:01:04: #2 You may need to consider one of the other alternative d(s): 81,302,462,542 WARNING @ Sat, 24 Aug 2019 19:01:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:01:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:01:09: 9000000 INFO @ Sat, 24 Aug 2019 19:01:17: 10000000 INFO @ Sat, 24 Aug 2019 19:01:25: 11000000 INFO @ Sat, 24 Aug 2019 19:01:34: 12000000 INFO @ Sat, 24 Aug 2019 19:01:34: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:01:42: 13000000 INFO @ Sat, 24 Aug 2019 19:01:45: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:01:45: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:01:45: #1 total tags in treatment: 13270998 INFO @ Sat, 24 Aug 2019 19:01:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:01:45: #1 tags after filtering in treatment: 13270869 INFO @ Sat, 24 Aug 2019 19:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:45: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:01:48: #2 number of paired peaks: 32505 INFO @ Sat, 24 Aug 2019 19:01:48: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:49: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:49: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:49: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:49: #2 predicted fragment length is 81 bps INFO @ Sat, 24 Aug 2019 19:01:49: #2 alternative fragment length(s) may be 81,302,462,542 bps INFO @ Sat, 24 Aug 2019 19:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.20_model.r WARNING @ Sat, 24 Aug 2019 19:01:49: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:01:49: #2 You may need to consider one of the other alternative d(s): 81,302,462,542 WARNING @ Sat, 24 Aug 2019 19:01:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:01:49: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.05_summits.bed INFO @ Sat, 24 Aug 2019 19:01:57: Done! pass1 - making usageList (112 chroms): 5 millis pass2 - checking and writing primary data (8778 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.10_summits.bed INFO @ Sat, 24 Aug 2019 19:02:08: Done! pass1 - making usageList (78 chroms): 2 millis pass2 - checking and writing primary data (1871 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:02:32: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349435/SRX349435.20_summits.bed INFO @ Sat, 24 Aug 2019 19:02:53: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (575 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。