Job ID = 4288883 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:35:39 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 ) 2019-12-10T03:35:39 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 ) 2019-12-10T03:35:39 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 : 29,513,358 reads read : 59,026,716 reads written : 29,513,358 reads 0-length : 29,513,358 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:25:32 29513358 reads; of these: 29513358 (100.00%) were unpaired; of these: 2499621 (8.47%) aligned 0 times 20411511 (69.16%) aligned exactly 1 time 6602226 (22.37%) aligned >1 times 91.53% overall alignment rate Time searching: 00:25:41 Overall time: 00:25:41 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 12 files... [bam_rmdupse_core] 8126971 / 27013737 = 0.3008 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.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 13:09:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:09:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:10:02: 1000000 INFO @ Tue, 10 Dec 2019 13:10:11: 2000000 INFO @ Tue, 10 Dec 2019 13:10:19: 3000000 INFO @ Tue, 10 Dec 2019 13:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.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 13:10:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:10:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:10:29: 4000000 INFO @ Tue, 10 Dec 2019 13:10:32: 1000000 INFO @ Tue, 10 Dec 2019 13:10:39: 5000000 INFO @ Tue, 10 Dec 2019 13:10:42: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:10:49: 6000000 INFO @ Tue, 10 Dec 2019 13:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.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 13:10:52: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:10:52: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:10:53: 3000000 INFO @ Tue, 10 Dec 2019 13:10:59: 7000000 INFO @ Tue, 10 Dec 2019 13:11:02: 1000000 INFO @ Tue, 10 Dec 2019 13:11:03: 4000000 INFO @ Tue, 10 Dec 2019 13:11:09: 8000000 INFO @ Tue, 10 Dec 2019 13:11:12: 2000000 INFO @ Tue, 10 Dec 2019 13:11:14: 5000000 INFO @ Tue, 10 Dec 2019 13:11:21: 9000000 INFO @ Tue, 10 Dec 2019 13:11:23: 3000000 INFO @ Tue, 10 Dec 2019 13:11:26: 6000000 INFO @ Tue, 10 Dec 2019 13:11:33: 4000000 INFO @ Tue, 10 Dec 2019 13:11:34: 10000000 INFO @ Tue, 10 Dec 2019 13:11:38: 7000000 INFO @ Tue, 10 Dec 2019 13:11:44: 5000000 INFO @ Tue, 10 Dec 2019 13:11:46: 11000000 INFO @ Tue, 10 Dec 2019 13:11:50: 8000000 INFO @ Tue, 10 Dec 2019 13:11:54: 6000000 INFO @ Tue, 10 Dec 2019 13:11:58: 12000000 INFO @ Tue, 10 Dec 2019 13:12:03: 9000000 INFO @ Tue, 10 Dec 2019 13:12:05: 7000000 INFO @ Tue, 10 Dec 2019 13:12:10: 13000000 INFO @ Tue, 10 Dec 2019 13:12:15: 8000000 INFO @ Tue, 10 Dec 2019 13:12:15: 10000000 INFO @ Tue, 10 Dec 2019 13:12:22: 14000000 INFO @ Tue, 10 Dec 2019 13:12:27: 9000000 INFO @ Tue, 10 Dec 2019 13:12:28: 11000000 INFO @ Tue, 10 Dec 2019 13:12:35: 15000000 INFO @ Tue, 10 Dec 2019 13:12:38: 10000000 INFO @ Tue, 10 Dec 2019 13:12:41: 12000000 INFO @ Tue, 10 Dec 2019 13:12:47: 16000000 INFO @ Tue, 10 Dec 2019 13:12:49: 11000000 INFO @ Tue, 10 Dec 2019 13:12:53: 13000000 INFO @ Tue, 10 Dec 2019 13:12:59: 12000000 INFO @ Tue, 10 Dec 2019 13:13:00: 17000000 INFO @ Tue, 10 Dec 2019 13:13:05: 14000000 INFO @ Tue, 10 Dec 2019 13:13:10: 13000000 INFO @ Tue, 10 Dec 2019 13:13:12: 18000000 INFO @ Tue, 10 Dec 2019 13:13:17: 15000000 INFO @ Tue, 10 Dec 2019 13:13:20: 14000000 INFO @ Tue, 10 Dec 2019 13:13:23: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:13:23: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:13:23: #1 total tags in treatment: 18886766 INFO @ Tue, 10 Dec 2019 13:13:23: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:13:23: #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 13:13:24: #1 tags after filtering in treatment: 18886602 INFO @ Tue, 10 Dec 2019 13:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:13:24: #1 finished! INFO @ Tue, 10 Dec 2019 13:13:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:13:29: 16000000 INFO @ Tue, 10 Dec 2019 13:13:29: #2 number of paired peaks: 100569 INFO @ Tue, 10 Dec 2019 13:13:29: start model_add_line... INFO @ Tue, 10 Dec 2019 13:13:30: start X-correlation... INFO @ Tue, 10 Dec 2019 13:13:30: end of X-cor INFO @ Tue, 10 Dec 2019 13:13:30: #2 finished! INFO @ Tue, 10 Dec 2019 13:13:30: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:13:30: #2 alternative fragment length(s) may be 3,154 bps INFO @ Tue, 10 Dec 2019 13:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.05_model.r INFO @ Tue, 10 Dec 2019 13:13:30: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:13:31: 15000000 INFO @ Tue, 10 Dec 2019 13:13:39: 17000000 INFO @ Tue, 10 Dec 2019 13:13:41: 16000000 INFO @ Tue, 10 Dec 2019 13:13:49: 18000000 INFO @ Tue, 10 Dec 2019 13:13:51: 17000000 INFO @ Tue, 10 Dec 2019 13:13:58: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:13:58: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:13:58: #1 total tags in treatment: 18886766 INFO @ Tue, 10 Dec 2019 13:13:58: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:13:58: #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 13:13:59: #1 tags after filtering in treatment: 18886602 INFO @ Tue, 10 Dec 2019 13:13:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:13:59: #1 finished! INFO @ Tue, 10 Dec 2019 13:13:59: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:14:01: 18000000 INFO @ Tue, 10 Dec 2019 13:14:05: #2 number of paired peaks: 100569 INFO @ Tue, 10 Dec 2019 13:14:05: start model_add_line... INFO @ Tue, 10 Dec 2019 13:14:05: start X-correlation... INFO @ Tue, 10 Dec 2019 13:14:05: end of X-cor INFO @ Tue, 10 Dec 2019 13:14:05: #2 finished! INFO @ Tue, 10 Dec 2019 13:14:05: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:14:05: #2 alternative fragment length(s) may be 3,154 bps INFO @ Tue, 10 Dec 2019 13:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.10_model.r INFO @ Tue, 10 Dec 2019 13:14:05: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:14:09: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:14:09: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:14:09: #1 total tags in treatment: 18886766 INFO @ Tue, 10 Dec 2019 13:14:09: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:14:09: #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 13:14:09: #1 tags after filtering in treatment: 18886602 INFO @ Tue, 10 Dec 2019 13:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:14:09: #1 finished! INFO @ Tue, 10 Dec 2019 13:14:09: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:14:15: #2 number of paired peaks: 100569 INFO @ Tue, 10 Dec 2019 13:14:15: start model_add_line... INFO @ Tue, 10 Dec 2019 13:14:15: start X-correlation... INFO @ Tue, 10 Dec 2019 13:14:15: end of X-cor INFO @ Tue, 10 Dec 2019 13:14:15: #2 finished! INFO @ Tue, 10 Dec 2019 13:14:15: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:14:15: #2 alternative fragment length(s) may be 3,154 bps INFO @ Tue, 10 Dec 2019 13:14:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.20_model.r INFO @ Tue, 10 Dec 2019 13:14:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:14:30: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.05_summits.bed INFO @ Tue, 10 Dec 2019 13:15:02: Done! pass1 - making usageList (107 chroms): 6 millis pass2 - checking and writing primary data (12997 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:15:06: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:15:16: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.10_summits.bed INFO @ Tue, 10 Dec 2019 13:15:37: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (2842 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779824/SRX4779824.20_summits.bed INFO @ Tue, 10 Dec 2019 13:15:47: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (349 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。