Job ID = 2001138 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:18:31 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T18:18:31 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/era0/ERR/ERR039/ERR039156' 2019-07-04T18:18:31 fasterq-dump.2.9.6 err: invalid accession 'ERR039156' 2019-07-04T18:22:18 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 ) 2019-07-04T18:24:46 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 ) 2019-07-04T18:24:46 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 ) 2019-07-04T18:24:50 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 ) 2019-07-04T18:24:52 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 : 18,368,654 reads read : 18,368,654 reads written : 18,368,654 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:34 18368654 reads; of these: 18368654 (100.00%) were unpaired; of these: 2023181 (11.01%) aligned 0 times 11169018 (60.80%) aligned exactly 1 time 5176455 (28.18%) aligned >1 times 88.99% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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] 5434823 / 16345473 = 0.3325 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 03:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.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 @ Fri, 05 Jul 2019 03:45:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:45:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.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 @ Fri, 05 Jul 2019 03:45:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:45:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.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 @ Fri, 05 Jul 2019 03:45:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:45:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:45:25: 1000000 INFO @ Fri, 05 Jul 2019 03:45:26: 1000000 INFO @ Fri, 05 Jul 2019 03:45:28: 1000000 INFO @ Fri, 05 Jul 2019 03:45:34: 2000000 INFO @ Fri, 05 Jul 2019 03:45:36: 2000000 INFO @ Fri, 05 Jul 2019 03:45:38: 2000000 INFO @ Fri, 05 Jul 2019 03:45:43: 3000000 INFO @ Fri, 05 Jul 2019 03:45:46: 3000000 INFO @ Fri, 05 Jul 2019 03:45:47: 3000000 INFO @ Fri, 05 Jul 2019 03:45:52: 4000000 INFO @ Fri, 05 Jul 2019 03:45:56: 4000000 INFO @ Fri, 05 Jul 2019 03:45:57: 4000000 INFO @ Fri, 05 Jul 2019 03:46:00: 5000000 INFO @ Fri, 05 Jul 2019 03:46:05: 5000000 INFO @ Fri, 05 Jul 2019 03:46:06: 5000000 INFO @ Fri, 05 Jul 2019 03:46:09: 6000000 INFO @ Fri, 05 Jul 2019 03:46:14: 6000000 INFO @ Fri, 05 Jul 2019 03:46:15: 6000000 INFO @ Fri, 05 Jul 2019 03:46:18: 7000000 INFO @ Fri, 05 Jul 2019 03:46:23: 7000000 INFO @ Fri, 05 Jul 2019 03:46:24: 7000000 INFO @ Fri, 05 Jul 2019 03:46:27: 8000000 INFO @ Fri, 05 Jul 2019 03:46:32: 8000000 INFO @ Fri, 05 Jul 2019 03:46:33: 8000000 INFO @ Fri, 05 Jul 2019 03:46:37: 9000000 INFO @ Fri, 05 Jul 2019 03:46:41: 9000000 INFO @ Fri, 05 Jul 2019 03:46:42: 9000000 INFO @ Fri, 05 Jul 2019 03:46:46: 10000000 INFO @ Fri, 05 Jul 2019 03:46:51: 10000000 INFO @ Fri, 05 Jul 2019 03:46:51: 10000000 INFO @ Fri, 05 Jul 2019 03:46:55: #1 tag size is determined as 41 bps INFO @ Fri, 05 Jul 2019 03:46:55: #1 tag size = 41 INFO @ Fri, 05 Jul 2019 03:46:55: #1 total tags in treatment: 10910650 INFO @ Fri, 05 Jul 2019 03:46:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:46:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 03:46:55: #1 tags after filtering in treatment: 10910469 INFO @ Fri, 05 Jul 2019 03:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:46:55: #1 finished! INFO @ Fri, 05 Jul 2019 03:46:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:46:57: #2 number of paired peaks: 7568 INFO @ Fri, 05 Jul 2019 03:46:57: start model_add_line... INFO @ Fri, 05 Jul 2019 03:46:57: start X-correlation... INFO @ Fri, 05 Jul 2019 03:46:57: end of X-cor INFO @ Fri, 05 Jul 2019 03:46:57: #2 finished! INFO @ Fri, 05 Jul 2019 03:46:57: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 03:46:57: #2 alternative fragment length(s) may be 41,217,396,503,578 bps INFO @ Fri, 05 Jul 2019 03:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.05_model.r WARNING @ Fri, 05 Jul 2019 03:46:57: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:46:57: #2 You may need to consider one of the other alternative d(s): 41,217,396,503,578 WARNING @ Fri, 05 Jul 2019 03:46:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 03:46:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:46:59: #1 tag size is determined as 41 bps INFO @ Fri, 05 Jul 2019 03:46:59: #1 tag size = 41 INFO @ Fri, 05 Jul 2019 03:46:59: #1 total tags in treatment: 10910650 INFO @ Fri, 05 Jul 2019 03:46:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:46:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 03:46:59: #1 tag size is determined as 41 bps INFO @ Fri, 05 Jul 2019 03:46:59: #1 tag size = 41 INFO @ Fri, 05 Jul 2019 03:46:59: #1 total tags in treatment: 10910650 INFO @ Fri, 05 Jul 2019 03:46:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:46:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 03:47:00: #1 tags after filtering in treatment: 10910469 INFO @ Fri, 05 Jul 2019 03:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:47:00: #1 finished! INFO @ Fri, 05 Jul 2019 03:47:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:47:00: #1 tags after filtering in treatment: 10910469 INFO @ Fri, 05 Jul 2019 03:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:47:00: #1 finished! INFO @ Fri, 05 Jul 2019 03:47:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:47:02: #2 number of paired peaks: 7568 INFO @ Fri, 05 Jul 2019 03:47:02: start model_add_line... INFO @ Fri, 05 Jul 2019 03:47:02: #2 number of paired peaks: 7568 INFO @ Fri, 05 Jul 2019 03:47:02: start model_add_line... INFO @ Fri, 05 Jul 2019 03:47:02: start X-correlation... INFO @ Fri, 05 Jul 2019 03:47:02: end of X-cor INFO @ Fri, 05 Jul 2019 03:47:02: #2 finished! INFO @ Fri, 05 Jul 2019 03:47:02: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 03:47:02: #2 alternative fragment length(s) may be 41,217,396,503,578 bps INFO @ Fri, 05 Jul 2019 03:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.10_model.r INFO @ Fri, 05 Jul 2019 03:47:02: start X-correlation... WARNING @ Fri, 05 Jul 2019 03:47:02: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:47:02: #2 You may need to consider one of the other alternative d(s): 41,217,396,503,578 WARNING @ Fri, 05 Jul 2019 03:47:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 03:47:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:47:02: end of X-cor INFO @ Fri, 05 Jul 2019 03:47:02: #2 finished! INFO @ Fri, 05 Jul 2019 03:47:02: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 03:47:02: #2 alternative fragment length(s) may be 41,217,396,503,578 bps INFO @ Fri, 05 Jul 2019 03:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.20_model.r WARNING @ Fri, 05 Jul 2019 03:47:02: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 03:47:02: #2 You may need to consider one of the other alternative d(s): 41,217,396,503,578 WARNING @ Fri, 05 Jul 2019 03:47:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 03:47:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:47:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.05_summits.bed INFO @ Fri, 05 Jul 2019 03:47:56: Done! pass1 - making usageList (61 chroms): 3 millis pass2 - checking and writing primary data (1820 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.20_summits.bed INFO @ Fri, 05 Jul 2019 03:47:58: Done! INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX016347/ERX016347.10_summits.bed INFO @ Fri, 05 Jul 2019 03:47:59: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (513 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (1151 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。