Job ID = 4178534 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:41:38 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 ) 2019-12-05T03:44:05 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 ) 2019-12-05T03:44:05 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 : 23,617,781 reads read : 23,617,781 reads written : 23,617,781 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:16 23617781 reads; of these: 23617781 (100.00%) were unpaired; of these: 3025875 (12.81%) aligned 0 times 16085772 (68.11%) aligned exactly 1 time 4506134 (19.08%) aligned >1 times 87.19% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6693632 / 20591906 = 0.3251 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:09:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:09:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:09:43: 1000000 INFO @ Thu, 05 Dec 2019 13:09:49: 2000000 INFO @ Thu, 05 Dec 2019 13:09:55: 3000000 INFO @ Thu, 05 Dec 2019 13:10:01: 4000000 INFO @ Thu, 05 Dec 2019 13:10:06: 5000000 INFO @ Thu, 05 Dec 2019 13:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:10:07: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:07: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:12: 6000000 INFO @ Thu, 05 Dec 2019 13:10:14: 1000000 INFO @ Thu, 05 Dec 2019 13:10:18: 7000000 INFO @ Thu, 05 Dec 2019 13:10:20: 2000000 INFO @ Thu, 05 Dec 2019 13:10:24: 8000000 INFO @ Thu, 05 Dec 2019 13:10:26: 3000000 INFO @ Thu, 05 Dec 2019 13:10:30: 9000000 INFO @ Thu, 05 Dec 2019 13:10:32: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:10:36: 10000000 INFO @ Thu, 05 Dec 2019 13:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:10:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:38: 5000000 INFO @ Thu, 05 Dec 2019 13:10:42: 11000000 INFO @ Thu, 05 Dec 2019 13:10:44: 1000000 INFO @ Thu, 05 Dec 2019 13:10:44: 6000000 INFO @ Thu, 05 Dec 2019 13:10:48: 12000000 INFO @ Thu, 05 Dec 2019 13:10:50: 7000000 INFO @ Thu, 05 Dec 2019 13:10:50: 2000000 INFO @ Thu, 05 Dec 2019 13:10:54: 13000000 INFO @ Thu, 05 Dec 2019 13:10:56: 8000000 INFO @ Thu, 05 Dec 2019 13:10:57: 3000000 INFO @ Thu, 05 Dec 2019 13:10:59: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:10:59: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:10:59: #1 total tags in treatment: 13898274 INFO @ Thu, 05 Dec 2019 13:10:59: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:10:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:00: #1 tags after filtering in treatment: 13898274 INFO @ Thu, 05 Dec 2019 13:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:11:00: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:00: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:01: #2 number of paired peaks: 1581 INFO @ Thu, 05 Dec 2019 13:11:01: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:01: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:01: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:01: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:01: #2 predicted fragment length is 164 bps INFO @ Thu, 05 Dec 2019 13:11:01: #2 alternative fragment length(s) may be 0,64,164,193,220,265,285,323 bps INFO @ Thu, 05 Dec 2019 13:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.05_model.r INFO @ Thu, 05 Dec 2019 13:11:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:02: 9000000 INFO @ Thu, 05 Dec 2019 13:11:02: 4000000 INFO @ Thu, 05 Dec 2019 13:11:08: 5000000 INFO @ Thu, 05 Dec 2019 13:11:08: 10000000 INFO @ Thu, 05 Dec 2019 13:11:14: 6000000 INFO @ Thu, 05 Dec 2019 13:11:14: 11000000 INFO @ Thu, 05 Dec 2019 13:11:20: 7000000 INFO @ Thu, 05 Dec 2019 13:11:20: 12000000 INFO @ Thu, 05 Dec 2019 13:11:26: 8000000 INFO @ Thu, 05 Dec 2019 13:11:26: 13000000 INFO @ Thu, 05 Dec 2019 13:11:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:11:32: 9000000 INFO @ Thu, 05 Dec 2019 13:11:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:11:32: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:11:32: #1 total tags in treatment: 13898274 INFO @ Thu, 05 Dec 2019 13:11:32: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:32: #1 tags after filtering in treatment: 13898274 INFO @ Thu, 05 Dec 2019 13:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:11:32: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:33: #2 number of paired peaks: 1581 INFO @ Thu, 05 Dec 2019 13:11:33: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:33: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:33: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:33: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:33: #2 predicted fragment length is 164 bps INFO @ Thu, 05 Dec 2019 13:11:33: #2 alternative fragment length(s) may be 0,64,164,193,220,265,285,323 bps INFO @ Thu, 05 Dec 2019 13:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.10_model.r INFO @ Thu, 05 Dec 2019 13:11:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:37: 10000000 INFO @ Thu, 05 Dec 2019 13:11:43: 11000000 INFO @ Thu, 05 Dec 2019 13:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.05_summits.bed INFO @ Thu, 05 Dec 2019 13:11:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2436 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:11:48: 12000000 INFO @ Thu, 05 Dec 2019 13:11:54: 13000000 INFO @ Thu, 05 Dec 2019 13:11:59: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:11:59: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:11:59: #1 total tags in treatment: 13898274 INFO @ Thu, 05 Dec 2019 13:11:59: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:59: #1 tags after filtering in treatment: 13898274 INFO @ Thu, 05 Dec 2019 13:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:11:59: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:59: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:12:00: #2 number of paired peaks: 1581 INFO @ Thu, 05 Dec 2019 13:12:00: start model_add_line... INFO @ Thu, 05 Dec 2019 13:12:00: start X-correlation... INFO @ Thu, 05 Dec 2019 13:12:00: end of X-cor INFO @ Thu, 05 Dec 2019 13:12:00: #2 finished! INFO @ Thu, 05 Dec 2019 13:12:00: #2 predicted fragment length is 164 bps INFO @ Thu, 05 Dec 2019 13:12:00: #2 alternative fragment length(s) may be 0,64,164,193,220,265,285,323 bps INFO @ Thu, 05 Dec 2019 13:12:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.20_model.r INFO @ Thu, 05 Dec 2019 13:12:00: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:12:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:12:02: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.10_summits.bed INFO @ Thu, 05 Dec 2019 13:12:15: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1051 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:12:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717050/SRX5717050.20_summits.bed INFO @ Thu, 05 Dec 2019 13:12:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (380 records, 4 fields): 168 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。