Job ID = 4288848 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:19:35 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 : 13,510,396 reads read : 27,020,792 reads written : 13,510,396 reads 0-length : 13,510,396 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: 00:13:27 13510396 reads; of these: 13510396 (100.00%) were unpaired; of these: 343265 (2.54%) aligned 0 times 9141178 (67.66%) aligned exactly 1 time 4025953 (29.80%) aligned >1 times 97.46% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 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 8 files... [bam_rmdupse_core] 543244 / 13167131 = 0.0413 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.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 12:39:54: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:54: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:03: 1000000 INFO @ Tue, 10 Dec 2019 12:40:12: 2000000 INFO @ Tue, 10 Dec 2019 12:40:20: 3000000 INFO @ Tue, 10 Dec 2019 12:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.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 12:40:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:40:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:28: 4000000 INFO @ Tue, 10 Dec 2019 12:40:33: 1000000 INFO @ Tue, 10 Dec 2019 12:40:37: 5000000 INFO @ Tue, 10 Dec 2019 12:40:42: 2000000 INFO @ Tue, 10 Dec 2019 12:40:45: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:40:52: 3000000 INFO @ Tue, 10 Dec 2019 12:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.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 12:40:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:40:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:54: 7000000 INFO @ Tue, 10 Dec 2019 12:41:02: 8000000 INFO @ Tue, 10 Dec 2019 12:41:03: 4000000 INFO @ Tue, 10 Dec 2019 12:41:04: 1000000 INFO @ Tue, 10 Dec 2019 12:41:11: 9000000 INFO @ Tue, 10 Dec 2019 12:41:14: 5000000 INFO @ Tue, 10 Dec 2019 12:41:16: 2000000 INFO @ Tue, 10 Dec 2019 12:41:20: 10000000 INFO @ Tue, 10 Dec 2019 12:41:26: 6000000 INFO @ Tue, 10 Dec 2019 12:41:28: 3000000 INFO @ Tue, 10 Dec 2019 12:41:28: 11000000 INFO @ Tue, 10 Dec 2019 12:41:37: 12000000 INFO @ Tue, 10 Dec 2019 12:41:37: 7000000 INFO @ Tue, 10 Dec 2019 12:41:39: 4000000 INFO @ Tue, 10 Dec 2019 12:41:43: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:43: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:43: #1 total tags in treatment: 12623887 INFO @ Tue, 10 Dec 2019 12:41:43: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:43: #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 12:41:43: #1 tags after filtering in treatment: 12623718 INFO @ Tue, 10 Dec 2019 12:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:43: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:43: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:45: #2 number of paired peaks: 5160 INFO @ Tue, 10 Dec 2019 12:41:45: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:45: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:45: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:45: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:45: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:45: #2 alternative fragment length(s) may be 51,232,414 bps INFO @ Tue, 10 Dec 2019 12:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.05_model.r WARNING @ Tue, 10 Dec 2019 12:41:45: #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 12:41:45: #2 You may need to consider one of the other alternative d(s): 51,232,414 WARNING @ Tue, 10 Dec 2019 12:41:45: #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 12:41:45: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:41:49: 8000000 INFO @ Tue, 10 Dec 2019 12:41:51: 5000000 INFO @ Tue, 10 Dec 2019 12:42:01: 9000000 INFO @ Tue, 10 Dec 2019 12:42:04: 6000000 INFO @ Tue, 10 Dec 2019 12:42:12: 10000000 INFO @ Tue, 10 Dec 2019 12:42:14: 7000000 INFO @ Tue, 10 Dec 2019 12:42:23: 11000000 INFO @ Tue, 10 Dec 2019 12:42:25: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:42:25: 8000000 INFO @ Tue, 10 Dec 2019 12:42:34: 12000000 INFO @ Tue, 10 Dec 2019 12:42:36: 9000000 INFO @ Tue, 10 Dec 2019 12:42:41: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:42:41: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:42:41: #1 total tags in treatment: 12623887 INFO @ Tue, 10 Dec 2019 12:42:41: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:42:41: #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 12:42:41: #1 tags after filtering in treatment: 12623718 INFO @ Tue, 10 Dec 2019 12:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:42:41: #1 finished! INFO @ Tue, 10 Dec 2019 12:42:41: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:42:43: #2 number of paired peaks: 5160 INFO @ Tue, 10 Dec 2019 12:42:43: start model_add_line... INFO @ Tue, 10 Dec 2019 12:42:43: start X-correlation... INFO @ Tue, 10 Dec 2019 12:42:43: end of X-cor INFO @ Tue, 10 Dec 2019 12:42:43: #2 finished! INFO @ Tue, 10 Dec 2019 12:42:43: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:42:43: #2 alternative fragment length(s) may be 51,232,414 bps INFO @ Tue, 10 Dec 2019 12:42:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.10_model.r WARNING @ Tue, 10 Dec 2019 12:42:43: #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 12:42:43: #2 You may need to consider one of the other alternative d(s): 51,232,414 WARNING @ Tue, 10 Dec 2019 12:42:43: #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 12:42:43: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:42:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.05_summits.bed INFO @ Tue, 10 Dec 2019 12:42:45: Done! INFO @ Tue, 10 Dec 2019 12:42:46: 10000000 pass1 - making usageList (47 chroms): 3 millis pass2 - checking and writing primary data (1010 records, 4 fields): 430 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:42:55: 11000000 INFO @ Tue, 10 Dec 2019 12:43:05: 12000000 INFO @ Tue, 10 Dec 2019 12:43:11: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:43:11: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:43:11: #1 total tags in treatment: 12623887 INFO @ Tue, 10 Dec 2019 12:43:11: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:43:11: #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 12:43:11: #1 tags after filtering in treatment: 12623718 INFO @ Tue, 10 Dec 2019 12:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:43:11: #1 finished! INFO @ Tue, 10 Dec 2019 12:43:11: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:43:13: #2 number of paired peaks: 5160 INFO @ Tue, 10 Dec 2019 12:43:13: start model_add_line... INFO @ Tue, 10 Dec 2019 12:43:13: start X-correlation... INFO @ Tue, 10 Dec 2019 12:43:13: end of X-cor INFO @ Tue, 10 Dec 2019 12:43:13: #2 finished! INFO @ Tue, 10 Dec 2019 12:43:13: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:43:13: #2 alternative fragment length(s) may be 51,232,414 bps INFO @ Tue, 10 Dec 2019 12:43:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.20_model.r WARNING @ Tue, 10 Dec 2019 12:43:13: #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 12:43:13: #2 You may need to consider one of the other alternative d(s): 51,232,414 WARNING @ Tue, 10 Dec 2019 12:43:13: #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 12:43:13: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:43:23: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.10_summits.bed INFO @ Tue, 10 Dec 2019 12:43:43: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (595 records, 4 fields): 256 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:43:53: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654076/SRX4654076.20_summits.bed INFO @ Tue, 10 Dec 2019 12:44:13: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。