Job ID = 4288879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:35:20 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 : 32,796,671 reads read : 65,593,342 reads written : 32,796,671 reads 0-length : 32,796,671 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: 00:00:00 Multiseed full-index search: 00:28:12 32796671 reads; of these: 32796671 (100.00%) were unpaired; of these: 759964 (2.32%) aligned 0 times 22142447 (67.51%) aligned exactly 1 time 9894260 (30.17%) aligned >1 times 97.68% overall alignment rate Time searching: 00:28:15 Overall time: 00:28:15 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 16 files... [bam_rmdupse_core] 1068918 / 32036707 = 0.0334 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.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 13:16:51: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:16:51: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:17:00: 1000000 INFO @ Tue, 10 Dec 2019 13:17:09: 2000000 INFO @ Tue, 10 Dec 2019 13:17:17: 3000000 INFO @ Tue, 10 Dec 2019 13:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.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 13:17:21: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:17:21: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:17:25: 4000000 INFO @ Tue, 10 Dec 2019 13:17:33: 1000000 INFO @ Tue, 10 Dec 2019 13:17:34: 5000000 INFO @ Tue, 10 Dec 2019 13:17:43: 6000000 INFO @ Tue, 10 Dec 2019 13:17:44: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.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 13:17:51: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:17:51: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:17:52: 7000000 INFO @ Tue, 10 Dec 2019 13:17:55: 3000000 INFO @ Tue, 10 Dec 2019 13:18:01: 1000000 INFO @ Tue, 10 Dec 2019 13:18:02: 8000000 INFO @ Tue, 10 Dec 2019 13:18:07: 4000000 INFO @ Tue, 10 Dec 2019 13:18:11: 2000000 INFO @ Tue, 10 Dec 2019 13:18:12: 9000000 INFO @ Tue, 10 Dec 2019 13:18:18: 5000000 INFO @ Tue, 10 Dec 2019 13:18:20: 3000000 INFO @ Tue, 10 Dec 2019 13:18:21: 10000000 INFO @ Tue, 10 Dec 2019 13:18:29: 6000000 INFO @ Tue, 10 Dec 2019 13:18:30: 4000000 INFO @ Tue, 10 Dec 2019 13:18:31: 11000000 INFO @ Tue, 10 Dec 2019 13:18:40: 5000000 INFO @ Tue, 10 Dec 2019 13:18:41: 7000000 INFO @ Tue, 10 Dec 2019 13:18:41: 12000000 INFO @ Tue, 10 Dec 2019 13:18:50: 6000000 INFO @ Tue, 10 Dec 2019 13:18:51: 13000000 INFO @ Tue, 10 Dec 2019 13:18:53: 8000000 INFO @ Tue, 10 Dec 2019 13:18:59: 7000000 INFO @ Tue, 10 Dec 2019 13:19:01: 14000000 INFO @ Tue, 10 Dec 2019 13:19:05: 9000000 INFO @ Tue, 10 Dec 2019 13:19:09: 8000000 INFO @ Tue, 10 Dec 2019 13:19:11: 15000000 INFO @ Tue, 10 Dec 2019 13:19:17: 10000000 INFO @ Tue, 10 Dec 2019 13:19:19: 9000000 INFO @ Tue, 10 Dec 2019 13:19:21: 16000000 INFO @ Tue, 10 Dec 2019 13:19:28: 10000000 INFO @ Tue, 10 Dec 2019 13:19:28: 11000000 INFO @ Tue, 10 Dec 2019 13:19:31: 17000000 INFO @ Tue, 10 Dec 2019 13:19:37: 11000000 INFO @ Tue, 10 Dec 2019 13:19:40: 12000000 INFO @ Tue, 10 Dec 2019 13:19:41: 18000000 INFO @ Tue, 10 Dec 2019 13:19:47: 12000000 INFO @ Tue, 10 Dec 2019 13:19:51: 19000000 INFO @ Tue, 10 Dec 2019 13:19:51: 13000000 INFO @ Tue, 10 Dec 2019 13:19:56: 13000000 INFO @ Tue, 10 Dec 2019 13:20:01: 20000000 INFO @ Tue, 10 Dec 2019 13:20:03: 14000000 INFO @ Tue, 10 Dec 2019 13:20:06: 14000000 INFO @ Tue, 10 Dec 2019 13:20:12: 21000000 INFO @ Tue, 10 Dec 2019 13:20:16: 15000000 INFO @ Tue, 10 Dec 2019 13:20:16: 15000000 INFO @ Tue, 10 Dec 2019 13:20:22: 22000000 INFO @ Tue, 10 Dec 2019 13:20:27: 16000000 INFO @ Tue, 10 Dec 2019 13:20:29: 16000000 INFO @ Tue, 10 Dec 2019 13:20:32: 23000000 INFO @ Tue, 10 Dec 2019 13:20:37: 17000000 INFO @ Tue, 10 Dec 2019 13:20:42: 24000000 INFO @ Tue, 10 Dec 2019 13:20:42: 17000000 INFO @ Tue, 10 Dec 2019 13:20:47: 18000000 INFO @ Tue, 10 Dec 2019 13:20:52: 25000000 INFO @ Tue, 10 Dec 2019 13:20:55: 18000000 INFO @ Tue, 10 Dec 2019 13:20:57: 19000000 INFO @ Tue, 10 Dec 2019 13:21:02: 26000000 INFO @ Tue, 10 Dec 2019 13:21:08: 20000000 INFO @ Tue, 10 Dec 2019 13:21:08: 19000000 INFO @ Tue, 10 Dec 2019 13:21:13: 27000000 INFO @ Tue, 10 Dec 2019 13:21:19: 21000000 INFO @ Tue, 10 Dec 2019 13:21:24: 28000000 INFO @ Tue, 10 Dec 2019 13:21:24: 20000000 INFO @ Tue, 10 Dec 2019 13:21:30: 22000000 INFO @ Tue, 10 Dec 2019 13:21:33: 29000000 INFO @ Tue, 10 Dec 2019 13:21:39: 21000000 INFO @ Tue, 10 Dec 2019 13:21:40: 23000000 INFO @ Tue, 10 Dec 2019 13:21:43: 30000000 INFO @ Tue, 10 Dec 2019 13:21:50: 24000000 INFO @ Tue, 10 Dec 2019 13:21:52: 22000000 INFO @ Tue, 10 Dec 2019 13:21:52: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:21:52: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:21:52: #1 total tags in treatment: 30967789 INFO @ Tue, 10 Dec 2019 13:21:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:21:52: #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 13:21:53: #1 tags after filtering in treatment: 30967707 INFO @ Tue, 10 Dec 2019 13:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:21:53: #1 finished! INFO @ Tue, 10 Dec 2019 13:21:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:21:57: #2 number of paired peaks: 5957 INFO @ Tue, 10 Dec 2019 13:21:57: start model_add_line... INFO @ Tue, 10 Dec 2019 13:21:57: start X-correlation... INFO @ Tue, 10 Dec 2019 13:21:57: end of X-cor INFO @ Tue, 10 Dec 2019 13:21:57: #2 finished! INFO @ Tue, 10 Dec 2019 13:21:57: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:21:57: #2 alternative fragment length(s) may be 50,204,396 bps INFO @ Tue, 10 Dec 2019 13:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.05_model.r WARNING @ Tue, 10 Dec 2019 13:21:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:21:57: #2 You may need to consider one of the other alternative d(s): 50,204,396 WARNING @ Tue, 10 Dec 2019 13:21:57: #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 13:21:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:21:59: 25000000 INFO @ Tue, 10 Dec 2019 13:22:07: 23000000 INFO @ Tue, 10 Dec 2019 13:22:09: 26000000 INFO @ Tue, 10 Dec 2019 13:22:18: 27000000 INFO @ Tue, 10 Dec 2019 13:22:19: 24000000 INFO @ Tue, 10 Dec 2019 13:22:28: 28000000 INFO @ Tue, 10 Dec 2019 13:22:31: 25000000 INFO @ Tue, 10 Dec 2019 13:22:37: 29000000 INFO @ Tue, 10 Dec 2019 13:22:44: 26000000 INFO @ Tue, 10 Dec 2019 13:22:47: 30000000 INFO @ Tue, 10 Dec 2019 13:22:57: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:22:57: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:22:57: #1 total tags in treatment: 30967789 INFO @ Tue, 10 Dec 2019 13:22:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:57: #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 13:22:57: 27000000 INFO @ Tue, 10 Dec 2019 13:22:57: #1 tags after filtering in treatment: 30967707 INFO @ Tue, 10 Dec 2019 13:22:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:57: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:23:01: #2 number of paired peaks: 5957 INFO @ Tue, 10 Dec 2019 13:23:01: start model_add_line... INFO @ Tue, 10 Dec 2019 13:23:01: start X-correlation... INFO @ Tue, 10 Dec 2019 13:23:01: end of X-cor INFO @ Tue, 10 Dec 2019 13:23:01: #2 finished! INFO @ Tue, 10 Dec 2019 13:23:01: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:23:01: #2 alternative fragment length(s) may be 50,204,396 bps INFO @ Tue, 10 Dec 2019 13:23:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.20_model.r WARNING @ Tue, 10 Dec 2019 13:23:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:23:01: #2 You may need to consider one of the other alternative d(s): 50,204,396 WARNING @ Tue, 10 Dec 2019 13:23:01: #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 13:23:01: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:23:09: 28000000 INFO @ Tue, 10 Dec 2019 13:23:21: 29000000 INFO @ Tue, 10 Dec 2019 13:23:32: 30000000 INFO @ Tue, 10 Dec 2019 13:23:33: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:23:44: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:23:44: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:23:44: #1 total tags in treatment: 30967789 INFO @ Tue, 10 Dec 2019 13:23:44: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:23:44: #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 13:23:45: #1 tags after filtering in treatment: 30967707 INFO @ Tue, 10 Dec 2019 13:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:23:45: #1 finished! INFO @ Tue, 10 Dec 2019 13:23:45: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:23:48: #2 number of paired peaks: 5957 INFO @ Tue, 10 Dec 2019 13:23:48: start model_add_line... INFO @ Tue, 10 Dec 2019 13:23:48: start X-correlation... INFO @ Tue, 10 Dec 2019 13:23:48: end of X-cor INFO @ Tue, 10 Dec 2019 13:23:48: #2 finished! INFO @ Tue, 10 Dec 2019 13:23:48: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:23:48: #2 alternative fragment length(s) may be 50,204,396 bps INFO @ Tue, 10 Dec 2019 13:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.10_model.r WARNING @ Tue, 10 Dec 2019 13:23:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:23:48: #2 You may need to consider one of the other alternative d(s): 50,204,396 WARNING @ Tue, 10 Dec 2019 13:23:48: #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 13:23:48: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:24:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:24:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:24:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.05_summits.bed INFO @ Tue, 10 Dec 2019 13:24:22: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (1909 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:24:37: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:25:25: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:25:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:25:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:25:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.20_summits.bed INFO @ Tue, 10 Dec 2019 13:25:25: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (542 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779823/SRX4779823.10_summits.bed INFO @ Tue, 10 Dec 2019 13:26:13: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。