Job ID = 4288943 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:41:44 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 ) 2019-12-10T03:41:44 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 : 8,762,742 reads read : 17,525,484 reads written : 8,762,742 reads 0-length : 8,762,742 spots read : 9,699,600 reads read : 19,399,200 reads written : 9,699,600 reads 0-length : 9,699,600 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:35 18462342 reads; of these: 18462342 (100.00%) were unpaired; of these: 1234497 (6.69%) aligned 0 times 14680504 (79.52%) aligned exactly 1 time 2547341 (13.80%) aligned >1 times 93.31% overall alignment rate Time searching: 00:15:36 Overall time: 00:15:36 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] 1781195 / 17227845 = 0.1034 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:19:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.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 13:19:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:19:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:19:50: 1000000 INFO @ Tue, 10 Dec 2019 13:20:00: 2000000 INFO @ Tue, 10 Dec 2019 13:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.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 13:20:09: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:09: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:10: 3000000 INFO @ Tue, 10 Dec 2019 13:20:19: 1000000 INFO @ Tue, 10 Dec 2019 13:20:20: 4000000 INFO @ Tue, 10 Dec 2019 13:20:27: 2000000 INFO @ Tue, 10 Dec 2019 13:20:31: 5000000 INFO @ Tue, 10 Dec 2019 13:20:36: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:20:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.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 13:20:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:40: 6000000 INFO @ Tue, 10 Dec 2019 13:20:45: 4000000 INFO @ Tue, 10 Dec 2019 13:20:50: 7000000 INFO @ Tue, 10 Dec 2019 13:20:52: 1000000 INFO @ Tue, 10 Dec 2019 13:20:53: 5000000 INFO @ Tue, 10 Dec 2019 13:21:00: 8000000 INFO @ Tue, 10 Dec 2019 13:21:02: 6000000 INFO @ Tue, 10 Dec 2019 13:21:03: 2000000 INFO @ Tue, 10 Dec 2019 13:21:11: 7000000 INFO @ Tue, 10 Dec 2019 13:21:11: 9000000 INFO @ Tue, 10 Dec 2019 13:21:15: 3000000 INFO @ Tue, 10 Dec 2019 13:21:20: 8000000 INFO @ Tue, 10 Dec 2019 13:21:22: 10000000 INFO @ Tue, 10 Dec 2019 13:21:27: 4000000 INFO @ Tue, 10 Dec 2019 13:21:29: 9000000 INFO @ Tue, 10 Dec 2019 13:21:33: 11000000 INFO @ Tue, 10 Dec 2019 13:21:38: 10000000 INFO @ Tue, 10 Dec 2019 13:21:38: 5000000 INFO @ Tue, 10 Dec 2019 13:21:43: 12000000 INFO @ Tue, 10 Dec 2019 13:21:46: 11000000 INFO @ Tue, 10 Dec 2019 13:21:49: 6000000 INFO @ Tue, 10 Dec 2019 13:21:53: 13000000 INFO @ Tue, 10 Dec 2019 13:21:56: 12000000 INFO @ Tue, 10 Dec 2019 13:22:00: 7000000 INFO @ Tue, 10 Dec 2019 13:22:05: 14000000 INFO @ Tue, 10 Dec 2019 13:22:06: 13000000 INFO @ Tue, 10 Dec 2019 13:22:11: 8000000 INFO @ Tue, 10 Dec 2019 13:22:15: 14000000 INFO @ Tue, 10 Dec 2019 13:22:16: 15000000 INFO @ Tue, 10 Dec 2019 13:22:21: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:22:21: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:22:21: #1 total tags in treatment: 15446650 INFO @ Tue, 10 Dec 2019 13:22:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:21: #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 13:22:21: #1 tags after filtering in treatment: 15446447 INFO @ Tue, 10 Dec 2019 13:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:21: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:23: 9000000 INFO @ Tue, 10 Dec 2019 13:22:25: 15000000 INFO @ Tue, 10 Dec 2019 13:22:26: #2 number of paired peaks: 79759 INFO @ Tue, 10 Dec 2019 13:22:26: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:26: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:26: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:26: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:26: #2 predicted fragment length is 185 bps INFO @ Tue, 10 Dec 2019 13:22:26: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 10 Dec 2019 13:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.05_model.r INFO @ Tue, 10 Dec 2019 13:22:26: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:22:30: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:22:30: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:22:30: #1 total tags in treatment: 15446650 INFO @ Tue, 10 Dec 2019 13:22:30: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:30: #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 13:22:30: #1 tags after filtering in treatment: 15446447 INFO @ Tue, 10 Dec 2019 13:22:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:30: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:30: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:33: 10000000 INFO @ Tue, 10 Dec 2019 13:22:34: #2 number of paired peaks: 79759 INFO @ Tue, 10 Dec 2019 13:22:34: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:35: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:35: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:35: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:35: #2 predicted fragment length is 185 bps INFO @ Tue, 10 Dec 2019 13:22:35: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 10 Dec 2019 13:22:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.10_model.r INFO @ Tue, 10 Dec 2019 13:22:35: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:22:44: 11000000 INFO @ Tue, 10 Dec 2019 13:22:53: 12000000 INFO @ Tue, 10 Dec 2019 13:23:01: 13000000 INFO @ Tue, 10 Dec 2019 13:23:10: 14000000 INFO @ Tue, 10 Dec 2019 13:23:17: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:23:19: 15000000 INFO @ Tue, 10 Dec 2019 13:23:22: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:23:22: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:23:22: #1 total tags in treatment: 15446650 INFO @ Tue, 10 Dec 2019 13:23:22: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:23:22: #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 13:23:23: #1 tags after filtering in treatment: 15446447 INFO @ Tue, 10 Dec 2019 13:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:23:23: #1 finished! INFO @ Tue, 10 Dec 2019 13:23:23: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:23:24: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:23:27: #2 number of paired peaks: 79759 INFO @ Tue, 10 Dec 2019 13:23:27: start model_add_line... INFO @ Tue, 10 Dec 2019 13:23:27: start X-correlation... INFO @ Tue, 10 Dec 2019 13:23:27: end of X-cor INFO @ Tue, 10 Dec 2019 13:23:27: #2 finished! INFO @ Tue, 10 Dec 2019 13:23:27: #2 predicted fragment length is 185 bps INFO @ Tue, 10 Dec 2019 13:23:27: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 10 Dec 2019 13:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.20_model.r INFO @ Tue, 10 Dec 2019 13:23:27: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:23:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.05_summits.bed INFO @ Tue, 10 Dec 2019 13:23:45: Done! pass1 - making usageList (107 chroms): 16 millis pass2 - checking and writing primary data (63620 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.10_summits.bed INFO @ Tue, 10 Dec 2019 13:23:50: Done! pass1 - making usageList (82 chroms): 7 millis pass2 - checking and writing primary data (36153 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:24:16: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460572/SRX5460572.20_summits.bed INFO @ Tue, 10 Dec 2019 13:24:42: Done! pass1 - making usageList (52 chroms): 6 millis pass2 - checking and writing primary data (15715 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。