Job ID = 4288914 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,356,770 reads read : 16,713,540 reads written : 8,356,770 reads 0-length : 8,356,770 2019-12-10T03:37:11 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 ) 2019-12-10T03:37:11 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 : 9,815,215 reads read : 19,630,430 reads written : 9,815,215 reads 0-length : 9,815,215 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: 00:16:51 18171985 reads; of these: 18171985 (100.00%) were unpaired; of these: 1347059 (7.41%) aligned 0 times 13569546 (74.67%) aligned exactly 1 time 3255380 (17.91%) aligned >1 times 92.59% overall alignment rate Time searching: 00:16:52 Overall time: 00:16:52 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] 4390594 / 16824926 = 0.2610 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.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 13:07:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:07:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:07:48: 1000000 INFO @ Tue, 10 Dec 2019 13:07:55: 2000000 INFO @ Tue, 10 Dec 2019 13:08:03: 3000000 INFO @ Tue, 10 Dec 2019 13:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.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 13:08:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:08:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:08:10: 4000000 INFO @ Tue, 10 Dec 2019 13:08:18: 5000000 INFO @ Tue, 10 Dec 2019 13:08:18: 1000000 INFO @ Tue, 10 Dec 2019 13:08:26: 6000000 INFO @ Tue, 10 Dec 2019 13:08:27: 2000000 INFO @ Tue, 10 Dec 2019 13:08:33: 7000000 INFO @ Tue, 10 Dec 2019 13:08:35: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.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 13:08:40: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:08:40: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:08:41: 8000000 INFO @ Tue, 10 Dec 2019 13:08:43: 4000000 INFO @ Tue, 10 Dec 2019 13:08:49: 9000000 INFO @ Tue, 10 Dec 2019 13:08:50: 1000000 INFO @ Tue, 10 Dec 2019 13:08:51: 5000000 INFO @ Tue, 10 Dec 2019 13:08:56: 10000000 INFO @ Tue, 10 Dec 2019 13:08:59: 6000000 INFO @ Tue, 10 Dec 2019 13:09:00: 2000000 INFO @ Tue, 10 Dec 2019 13:09:04: 11000000 INFO @ Tue, 10 Dec 2019 13:09:08: 7000000 INFO @ Tue, 10 Dec 2019 13:09:09: 3000000 INFO @ Tue, 10 Dec 2019 13:09:12: 12000000 INFO @ Tue, 10 Dec 2019 13:09:15: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:09:15: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:09:15: #1 total tags in treatment: 12434332 INFO @ Tue, 10 Dec 2019 13:09:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:09:15: #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 13:09:16: #1 tags after filtering in treatment: 12434114 INFO @ Tue, 10 Dec 2019 13:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:09:16: #1 finished! INFO @ Tue, 10 Dec 2019 13:09:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:09:16: 8000000 INFO @ Tue, 10 Dec 2019 13:09:19: #2 number of paired peaks: 46387 INFO @ Tue, 10 Dec 2019 13:09:19: start model_add_line... INFO @ Tue, 10 Dec 2019 13:09:19: start X-correlation... INFO @ Tue, 10 Dec 2019 13:09:19: end of X-cor INFO @ Tue, 10 Dec 2019 13:09:19: #2 finished! INFO @ Tue, 10 Dec 2019 13:09:19: #2 predicted fragment length is 175 bps INFO @ Tue, 10 Dec 2019 13:09:19: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 10 Dec 2019 13:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.05_model.r INFO @ Tue, 10 Dec 2019 13:09:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:09:19: 4000000 INFO @ Tue, 10 Dec 2019 13:09:24: 9000000 INFO @ Tue, 10 Dec 2019 13:09:29: 5000000 INFO @ Tue, 10 Dec 2019 13:09:32: 10000000 INFO @ Tue, 10 Dec 2019 13:09:38: 6000000 INFO @ Tue, 10 Dec 2019 13:09:40: 11000000 INFO @ Tue, 10 Dec 2019 13:09:48: 7000000 INFO @ Tue, 10 Dec 2019 13:09:49: 12000000 INFO @ Tue, 10 Dec 2019 13:09:52: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:09:52: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:09:52: #1 total tags in treatment: 12434332 INFO @ Tue, 10 Dec 2019 13:09:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:09:52: #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 13:09:53: #1 tags after filtering in treatment: 12434114 INFO @ Tue, 10 Dec 2019 13:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:09:53: #1 finished! INFO @ Tue, 10 Dec 2019 13:09:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:09:56: #2 number of paired peaks: 46387 INFO @ Tue, 10 Dec 2019 13:09:56: start model_add_line... INFO @ Tue, 10 Dec 2019 13:09:56: start X-correlation... INFO @ Tue, 10 Dec 2019 13:09:56: end of X-cor INFO @ Tue, 10 Dec 2019 13:09:56: #2 finished! INFO @ Tue, 10 Dec 2019 13:09:56: #2 predicted fragment length is 175 bps INFO @ Tue, 10 Dec 2019 13:09:56: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 10 Dec 2019 13:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.10_model.r INFO @ Tue, 10 Dec 2019 13:09:56: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:09:57: 8000000 INFO @ Tue, 10 Dec 2019 13:09:59: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:10:07: 9000000 INFO @ Tue, 10 Dec 2019 13:10:16: 10000000 INFO @ Tue, 10 Dec 2019 13:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.05_summits.bed INFO @ Tue, 10 Dec 2019 13:10:20: Done! pass1 - making usageList (93 chroms): 9 millis pass2 - checking and writing primary data (26018 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:10:25: 11000000 INFO @ Tue, 10 Dec 2019 13:10:35: 12000000 INFO @ Tue, 10 Dec 2019 13:10:36: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:10:39: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:10:39: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:10:39: #1 total tags in treatment: 12434332 INFO @ Tue, 10 Dec 2019 13:10:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:10:39: #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 13:10:39: #1 tags after filtering in treatment: 12434114 INFO @ Tue, 10 Dec 2019 13:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:10:39: #1 finished! INFO @ Tue, 10 Dec 2019 13:10:39: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:10:42: #2 number of paired peaks: 46387 INFO @ Tue, 10 Dec 2019 13:10:42: start model_add_line... INFO @ Tue, 10 Dec 2019 13:10:43: start X-correlation... INFO @ Tue, 10 Dec 2019 13:10:43: end of X-cor INFO @ Tue, 10 Dec 2019 13:10:43: #2 finished! INFO @ Tue, 10 Dec 2019 13:10:43: #2 predicted fragment length is 175 bps INFO @ Tue, 10 Dec 2019 13:10:43: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 10 Dec 2019 13:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.20_model.r INFO @ Tue, 10 Dec 2019 13:10:43: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:10:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.10_summits.bed INFO @ Tue, 10 Dec 2019 13:10:56: Done! pass1 - making usageList (56 chroms): 3 millis pass2 - checking and writing primary data (12320 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:11:23: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460562/SRX5460562.20_summits.bed INFO @ Tue, 10 Dec 2019 13:11:43: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (4348 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。