Job ID = 4288809 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:13:16 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 : 15,922,976 reads read : 31,845,952 reads written : 15,922,976 reads 0-length : 15,922,976 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:42 15922976 reads; of these: 15922976 (100.00%) were unpaired; of these: 9937994 (62.41%) aligned 0 times 4088906 (25.68%) aligned exactly 1 time 1896076 (11.91%) aligned >1 times 37.59% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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_rmdupse_core] 400215 / 5984982 = 0.0669 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.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 @ Tue, 10 Dec 2019 12:23:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:23:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:23:39: 1000000 INFO @ Tue, 10 Dec 2019 12:23:46: 2000000 INFO @ Tue, 10 Dec 2019 12:23:53: 3000000 INFO @ Tue, 10 Dec 2019 12:24:00: 4000000 INFO @ Tue, 10 Dec 2019 12:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.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 @ Tue, 10 Dec 2019 12:24:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:24:07: 5000000 INFO @ Tue, 10 Dec 2019 12:24:09: 1000000 INFO @ Tue, 10 Dec 2019 12:24:11: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:24:11: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:24:11: #1 total tags in treatment: 5584767 INFO @ Tue, 10 Dec 2019 12:24:11: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:24:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:24:12: #1 tags after filtering in treatment: 5584495 INFO @ Tue, 10 Dec 2019 12:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:24:12: #1 finished! INFO @ Tue, 10 Dec 2019 12:24:12: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:24:13: #2 number of paired peaks: 7516 INFO @ Tue, 10 Dec 2019 12:24:13: start model_add_line... INFO @ Tue, 10 Dec 2019 12:24:13: start X-correlation... INFO @ Tue, 10 Dec 2019 12:24:13: end of X-cor INFO @ Tue, 10 Dec 2019 12:24:13: #2 finished! INFO @ Tue, 10 Dec 2019 12:24:13: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:24:13: #2 alternative fragment length(s) may be 51,238 bps INFO @ Tue, 10 Dec 2019 12:24:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.05_model.r WARNING @ Tue, 10 Dec 2019 12:24:14: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:24:14: #2 You may need to consider one of the other alternative d(s): 51,238 WARNING @ Tue, 10 Dec 2019 12:24:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:24:14: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:24:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:24:16: 2000000 INFO @ Tue, 10 Dec 2019 12:24:24: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.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 @ Tue, 10 Dec 2019 12:24:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:24:32: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:24:32: 4000000 INFO @ Tue, 10 Dec 2019 12:24:39: 1000000 INFO @ Tue, 10 Dec 2019 12:24:40: 5000000 INFO @ Tue, 10 Dec 2019 12:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.05_summits.bed INFO @ Tue, 10 Dec 2019 12:24:40: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (663 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:24:45: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:24:45: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:24:45: #1 total tags in treatment: 5584767 INFO @ Tue, 10 Dec 2019 12:24:45: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:24:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:24:45: #1 tags after filtering in treatment: 5584495 INFO @ Tue, 10 Dec 2019 12:24:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:24:45: #1 finished! INFO @ Tue, 10 Dec 2019 12:24:45: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:24:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:24:46: 2000000 INFO @ Tue, 10 Dec 2019 12:24:47: #2 number of paired peaks: 7516 INFO @ Tue, 10 Dec 2019 12:24:47: start model_add_line... INFO @ Tue, 10 Dec 2019 12:24:47: start X-correlation... INFO @ Tue, 10 Dec 2019 12:24:47: end of X-cor INFO @ Tue, 10 Dec 2019 12:24:47: #2 finished! INFO @ Tue, 10 Dec 2019 12:24:47: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:24:47: #2 alternative fragment length(s) may be 51,238 bps INFO @ Tue, 10 Dec 2019 12:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.10_model.r WARNING @ Tue, 10 Dec 2019 12:24:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:24:47: #2 You may need to consider one of the other alternative d(s): 51,238 WARNING @ Tue, 10 Dec 2019 12:24:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:24:47: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:24:54: 3000000 INFO @ Tue, 10 Dec 2019 12:25:02: 4000000 INFO @ Tue, 10 Dec 2019 12:25:05: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:25:10: 5000000 INFO @ Tue, 10 Dec 2019 12:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.10_summits.bed INFO @ Tue, 10 Dec 2019 12:25:13: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:25:14: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:25:14: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:25:14: #1 total tags in treatment: 5584767 INFO @ Tue, 10 Dec 2019 12:25:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:25:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:25:14: #1 tags after filtering in treatment: 5584495 INFO @ Tue, 10 Dec 2019 12:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:25:14: #1 finished! INFO @ Tue, 10 Dec 2019 12:25:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:25:16: #2 number of paired peaks: 7516 INFO @ Tue, 10 Dec 2019 12:25:16: start model_add_line... INFO @ Tue, 10 Dec 2019 12:25:16: start X-correlation... INFO @ Tue, 10 Dec 2019 12:25:16: end of X-cor INFO @ Tue, 10 Dec 2019 12:25:16: #2 finished! INFO @ Tue, 10 Dec 2019 12:25:16: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:25:16: #2 alternative fragment length(s) may be 51,238 bps INFO @ Tue, 10 Dec 2019 12:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.20_model.r WARNING @ Tue, 10 Dec 2019 12:25:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:25:16: #2 You may need to consider one of the other alternative d(s): 51,238 WARNING @ Tue, 10 Dec 2019 12:25:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:25:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:25:34: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:25:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:25:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654067/SRX4654067.20_summits.bed INFO @ Tue, 10 Dec 2019 12:25:43: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (144 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。