Job ID = 2640425 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:34:19 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 ) 2019-08-24T07:34:49 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T07:39:35 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 ) 2019-08-24T07:40:23 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 ) 2019-08-24T07:40:36 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 ) 2019-08-24T07:40:55 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 : 109,989,957 reads read : 109,989,957 reads written : 109,989,957 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR980343.sra.cache’: 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: 00:00:01 Multiseed full-index search: 02:28:40 109989957 reads; of these: 109989957 (100.00%) were unpaired; of these: 30644296 (27.86%) aligned 0 times 61312721 (55.74%) aligned exactly 1 time 18032940 (16.40%) aligned >1 times 72.14% overall alignment rate Time searching: 02:28:45 Overall time: 02:28:45 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 36 files... [bam_rmdupse_core] 65610037 / 79345661 = 0.8269 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.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 @ Sat, 24 Aug 2019 19:30:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:30:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:30:32: 1000000 INFO @ Sat, 24 Aug 2019 19:30:40: 2000000 INFO @ Sat, 24 Aug 2019 19:30:48: 3000000 INFO @ Sat, 24 Aug 2019 19:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.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 @ Sat, 24 Aug 2019 19:30:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:30:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:30:56: 4000000 INFO @ Sat, 24 Aug 2019 19:31:03: 1000000 INFO @ Sat, 24 Aug 2019 19:31:04: 5000000 INFO @ Sat, 24 Aug 2019 19:31:12: 2000000 INFO @ Sat, 24 Aug 2019 19:31:12: 6000000 INFO @ Sat, 24 Aug 2019 19:31:21: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:31:21: 3000000 INFO @ Sat, 24 Aug 2019 19:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.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 @ Sat, 24 Aug 2019 19:31:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:31:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:31:30: 8000000 INFO @ Sat, 24 Aug 2019 19:31:31: 4000000 INFO @ Sat, 24 Aug 2019 19:31:34: 1000000 INFO @ Sat, 24 Aug 2019 19:31:39: 9000000 INFO @ Sat, 24 Aug 2019 19:31:41: 5000000 INFO @ Sat, 24 Aug 2019 19:31:44: 2000000 INFO @ Sat, 24 Aug 2019 19:31:49: 10000000 INFO @ Sat, 24 Aug 2019 19:31:50: 6000000 INFO @ Sat, 24 Aug 2019 19:31:53: 3000000 INFO @ Sat, 24 Aug 2019 19:31:58: 11000000 INFO @ Sat, 24 Aug 2019 19:31:59: 7000000 INFO @ Sat, 24 Aug 2019 19:32:01: 4000000 INFO @ Sat, 24 Aug 2019 19:32:08: 8000000 INFO @ Sat, 24 Aug 2019 19:32:08: 12000000 INFO @ Sat, 24 Aug 2019 19:32:10: 5000000 INFO @ Sat, 24 Aug 2019 19:32:17: 9000000 INFO @ Sat, 24 Aug 2019 19:32:17: 13000000 INFO @ Sat, 24 Aug 2019 19:32:18: 6000000 INFO @ Sat, 24 Aug 2019 19:32:24: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:32:24: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:32:24: #1 total tags in treatment: 13735624 INFO @ Sat, 24 Aug 2019 19:32:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:32:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:32:25: #1 tags after filtering in treatment: 13735488 INFO @ Sat, 24 Aug 2019 19:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:32:25: #1 finished! INFO @ Sat, 24 Aug 2019 19:32:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:32:26: 10000000 INFO @ Sat, 24 Aug 2019 19:32:27: 7000000 INFO @ Sat, 24 Aug 2019 19:32:28: #2 number of paired peaks: 22142 INFO @ Sat, 24 Aug 2019 19:32:28: start model_add_line... INFO @ Sat, 24 Aug 2019 19:32:28: start X-correlation... INFO @ Sat, 24 Aug 2019 19:32:28: end of X-cor INFO @ Sat, 24 Aug 2019 19:32:28: #2 finished! INFO @ Sat, 24 Aug 2019 19:32:28: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 19:32:28: #2 alternative fragment length(s) may be 51,185 bps INFO @ Sat, 24 Aug 2019 19:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.05_model.r WARNING @ Sat, 24 Aug 2019 19:32:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:32:28: #2 You may need to consider one of the other alternative d(s): 51,185 WARNING @ Sat, 24 Aug 2019 19:32:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:32:28: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:32:35: 8000000 INFO @ Sat, 24 Aug 2019 19:32:35: 11000000 INFO @ Sat, 24 Aug 2019 19:32:43: 9000000 INFO @ Sat, 24 Aug 2019 19:32:44: 12000000 INFO @ Sat, 24 Aug 2019 19:32:51: 10000000 INFO @ Sat, 24 Aug 2019 19:32:52: 13000000 INFO @ Sat, 24 Aug 2019 19:32:59: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:32:59: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:32:59: #1 total tags in treatment: 13735624 INFO @ Sat, 24 Aug 2019 19:32:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:32:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:32:59: 11000000 INFO @ Sat, 24 Aug 2019 19:32:59: #1 tags after filtering in treatment: 13735488 INFO @ Sat, 24 Aug 2019 19:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:32:59: #1 finished! INFO @ Sat, 24 Aug 2019 19:32:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:33:02: #2 number of paired peaks: 22142 INFO @ Sat, 24 Aug 2019 19:33:02: start model_add_line... INFO @ Sat, 24 Aug 2019 19:33:02: start X-correlation... INFO @ Sat, 24 Aug 2019 19:33:02: end of X-cor INFO @ Sat, 24 Aug 2019 19:33:02: #2 finished! INFO @ Sat, 24 Aug 2019 19:33:02: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 19:33:02: #2 alternative fragment length(s) may be 51,185 bps INFO @ Sat, 24 Aug 2019 19:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.10_model.r WARNING @ Sat, 24 Aug 2019 19:33:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:33:02: #2 You may need to consider one of the other alternative d(s): 51,185 WARNING @ Sat, 24 Aug 2019 19:33:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:33:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:33:07: 12000000 INFO @ Sat, 24 Aug 2019 19:33:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:33:15: 13000000 INFO @ Sat, 24 Aug 2019 19:33:21: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:33:21: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:33:21: #1 total tags in treatment: 13735624 INFO @ Sat, 24 Aug 2019 19:33:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:33:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:33:21: #1 tags after filtering in treatment: 13735488 INFO @ Sat, 24 Aug 2019 19:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:33:21: #1 finished! INFO @ Sat, 24 Aug 2019 19:33:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:33:24: #2 number of paired peaks: 22142 INFO @ Sat, 24 Aug 2019 19:33:24: start model_add_line... INFO @ Sat, 24 Aug 2019 19:33:24: start X-correlation... INFO @ Sat, 24 Aug 2019 19:33:24: end of X-cor INFO @ Sat, 24 Aug 2019 19:33:24: #2 finished! INFO @ Sat, 24 Aug 2019 19:33:24: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 19:33:24: #2 alternative fragment length(s) may be 51,185 bps INFO @ Sat, 24 Aug 2019 19:33:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.20_model.r WARNING @ Sat, 24 Aug 2019 19:33:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:33:25: #2 You may need to consider one of the other alternative d(s): 51,185 WARNING @ Sat, 24 Aug 2019 19:33:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:33:25: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:33:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:33:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:33:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.05_summits.bed INFO @ Sat, 24 Aug 2019 19:33:33: Done! pass1 - making usageList (172 chroms): 7 millis pass2 - checking and writing primary data (28430 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:33:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.10_summits.bed INFO @ Sat, 24 Aug 2019 19:34:07: Done! INFO @ Sat, 24 Aug 2019 19:34:07: #3 Call peaks for each chromosome... pass1 - making usageList (96 chroms): 4 millis pass2 - checking and writing primary data (6234 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349430/SRX349430.20_summits.bed INFO @ Sat, 24 Aug 2019 19:34:30: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (1406 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。