Job ID = 1292426 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T09:25:48 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T09:25:48 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra64/SRR/007120/SRR7291534' 2019-06-02T09:25:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291534' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:25:48 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:30:30 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T09:30:30 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra64/SRR/007120/SRR7291534' 2019-06-02T09:30:30 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291534' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:30:30 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 7,833,373 reads read : 15,666,746 reads written : 7,833,373 reads 0-length : 7,833,373 2019-06-02T09:35:46 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T09:35:46 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra64/SRR/007120/SRR7291535' 2019-06-02T09:35:46 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR7291535' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:35:46 fasterq-dump.2.9.6 err: invalid accession 'SRR7291535' spots read : 7,695,953 reads read : 15,391,906 reads written : 7,695,953 reads 0-length : 7,695,953 spots read : 7,810,811 reads read : 15,621,622 reads written : 7,810,811 reads 0-length : 7,810,811 spots read : 7,595,632 reads read : 15,191,264 reads written : 7,595,632 reads 0-length : 7,595,632 rm: cannot remove ‘fastqDump_tmp*’: 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: 00:12:09 30935769 reads; of these: 30935769 (100.00%) were unpaired; of these: 1386359 (4.48%) aligned 0 times 24605976 (79.54%) aligned exactly 1 time 4943434 (15.98%) aligned >1 times 95.52% overall alignment rate Time searching: 00:12:09 Overall time: 00:12:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5246493 / 29549410 = 0.1775 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 @ Sun, 02 Jun 2019 19:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:14:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:14:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:14:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:56: 1000000 INFO @ Sun, 02 Jun 2019 19:14:57: 1000000 INFO @ Sun, 02 Jun 2019 19:14:57: 1000000 INFO @ Sun, 02 Jun 2019 19:15:03: 2000000 INFO @ Sun, 02 Jun 2019 19:15:05: 2000000 INFO @ Sun, 02 Jun 2019 19:15:06: 2000000 INFO @ Sun, 02 Jun 2019 19:15:10: 3000000 INFO @ Sun, 02 Jun 2019 19:15:12: 3000000 INFO @ Sun, 02 Jun 2019 19:15:15: 3000000 INFO @ Sun, 02 Jun 2019 19:15:17: 4000000 INFO @ Sun, 02 Jun 2019 19:15:19: 4000000 INFO @ Sun, 02 Jun 2019 19:15:23: 4000000 INFO @ Sun, 02 Jun 2019 19:15:23: 5000000 INFO @ Sun, 02 Jun 2019 19:15:27: 5000000 INFO @ Sun, 02 Jun 2019 19:15:30: 6000000 INFO @ Sun, 02 Jun 2019 19:15:32: 5000000 INFO @ Sun, 02 Jun 2019 19:15:34: 6000000 INFO @ Sun, 02 Jun 2019 19:15:37: 7000000 INFO @ Sun, 02 Jun 2019 19:15:40: 6000000 INFO @ Sun, 02 Jun 2019 19:15:42: 7000000 INFO @ Sun, 02 Jun 2019 19:15:44: 8000000 INFO @ Sun, 02 Jun 2019 19:15:49: 7000000 INFO @ Sun, 02 Jun 2019 19:15:49: 8000000 INFO @ Sun, 02 Jun 2019 19:15:51: 9000000 INFO @ Sun, 02 Jun 2019 19:15:57: 9000000 INFO @ Sun, 02 Jun 2019 19:15:58: 8000000 INFO @ Sun, 02 Jun 2019 19:15:58: 10000000 INFO @ Sun, 02 Jun 2019 19:16:05: 10000000 INFO @ Sun, 02 Jun 2019 19:16:05: 11000000 INFO @ Sun, 02 Jun 2019 19:16:06: 9000000 INFO @ Sun, 02 Jun 2019 19:16:12: 12000000 INFO @ Sun, 02 Jun 2019 19:16:13: 11000000 INFO @ Sun, 02 Jun 2019 19:16:16: 10000000 INFO @ Sun, 02 Jun 2019 19:16:19: 13000000 INFO @ Sun, 02 Jun 2019 19:16:20: 12000000 INFO @ Sun, 02 Jun 2019 19:16:25: 11000000 INFO @ Sun, 02 Jun 2019 19:16:26: 14000000 INFO @ Sun, 02 Jun 2019 19:16:28: 13000000 INFO @ Sun, 02 Jun 2019 19:16:33: 15000000 INFO @ Sun, 02 Jun 2019 19:16:34: 12000000 INFO @ Sun, 02 Jun 2019 19:16:36: 14000000 INFO @ Sun, 02 Jun 2019 19:16:40: 16000000 INFO @ Sun, 02 Jun 2019 19:16:43: 13000000 INFO @ Sun, 02 Jun 2019 19:16:44: 15000000 INFO @ Sun, 02 Jun 2019 19:16:47: 17000000 INFO @ Sun, 02 Jun 2019 19:16:51: 16000000 INFO @ Sun, 02 Jun 2019 19:16:52: 14000000 INFO @ Sun, 02 Jun 2019 19:16:54: 18000000 INFO @ Sun, 02 Jun 2019 19:16:59: 17000000 INFO @ Sun, 02 Jun 2019 19:17:01: 15000000 INFO @ Sun, 02 Jun 2019 19:17:01: 19000000 INFO @ Sun, 02 Jun 2019 19:17:06: 18000000 INFO @ Sun, 02 Jun 2019 19:17:08: 20000000 INFO @ Sun, 02 Jun 2019 19:17:10: 16000000 INFO @ Sun, 02 Jun 2019 19:17:14: 19000000 INFO @ Sun, 02 Jun 2019 19:17:15: 21000000 INFO @ Sun, 02 Jun 2019 19:17:18: 17000000 INFO @ Sun, 02 Jun 2019 19:17:21: 20000000 INFO @ Sun, 02 Jun 2019 19:17:22: 22000000 INFO @ Sun, 02 Jun 2019 19:17:27: 18000000 INFO @ Sun, 02 Jun 2019 19:17:29: 23000000 INFO @ Sun, 02 Jun 2019 19:17:29: 21000000 INFO @ Sun, 02 Jun 2019 19:17:36: 24000000 INFO @ Sun, 02 Jun 2019 19:17:36: 19000000 INFO @ Sun, 02 Jun 2019 19:17:36: 22000000 INFO @ Sun, 02 Jun 2019 19:17:38: #1 tag size is determined as 67 bps INFO @ Sun, 02 Jun 2019 19:17:38: #1 tag size = 67 INFO @ Sun, 02 Jun 2019 19:17:38: #1 total tags in treatment: 24302917 INFO @ Sun, 02 Jun 2019 19:17:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:17:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:17:39: #1 tags after filtering in treatment: 24302917 INFO @ Sun, 02 Jun 2019 19:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:17:39: #1 finished! INFO @ Sun, 02 Jun 2019 19:17:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:17:41: #2 number of paired peaks: 142 WARNING @ Sun, 02 Jun 2019 19:17:41: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sun, 02 Jun 2019 19:17:41: start model_add_line... INFO @ Sun, 02 Jun 2019 19:17:41: start X-correlation... INFO @ Sun, 02 Jun 2019 19:17:41: end of X-cor INFO @ Sun, 02 Jun 2019 19:17:41: #2 finished! INFO @ Sun, 02 Jun 2019 19:17:41: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:17:41: #2 alternative fragment length(s) may be 1,25,44,60 bps INFO @ Sun, 02 Jun 2019 19:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.20_model.r WARNING @ Sun, 02 Jun 2019 19:17:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:17:41: #2 You may need to consider one of the other alternative d(s): 1,25,44,60 WARNING @ Sun, 02 Jun 2019 19:17:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:17:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:17:44: 23000000 INFO @ Sun, 02 Jun 2019 19:17:44: 20000000 INFO @ Sun, 02 Jun 2019 19:17:51: 24000000 INFO @ Sun, 02 Jun 2019 19:17:53: 21000000 INFO @ Sun, 02 Jun 2019 19:17:54: #1 tag size is determined as 67 bps INFO @ Sun, 02 Jun 2019 19:17:54: #1 tag size = 67 INFO @ Sun, 02 Jun 2019 19:17:54: #1 total tags in treatment: 24302917 INFO @ Sun, 02 Jun 2019 19:17:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:17:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:17:55: #1 tags after filtering in treatment: 24302917 INFO @ Sun, 02 Jun 2019 19:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:17:55: #1 finished! INFO @ Sun, 02 Jun 2019 19:17:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:17:57: #2 number of paired peaks: 142 WARNING @ Sun, 02 Jun 2019 19:17:57: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sun, 02 Jun 2019 19:17:57: start model_add_line... INFO @ Sun, 02 Jun 2019 19:17:57: start X-correlation... INFO @ Sun, 02 Jun 2019 19:17:57: end of X-cor INFO @ Sun, 02 Jun 2019 19:17:57: #2 finished! INFO @ Sun, 02 Jun 2019 19:17:57: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:17:57: #2 alternative fragment length(s) may be 1,25,44,60 bps INFO @ Sun, 02 Jun 2019 19:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.10_model.r WARNING @ Sun, 02 Jun 2019 19:17:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:17:57: #2 You may need to consider one of the other alternative d(s): 1,25,44,60 WARNING @ Sun, 02 Jun 2019 19:17:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:17:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:18:02: 22000000 INFO @ Sun, 02 Jun 2019 19:18:10: 23000000 INFO @ Sun, 02 Jun 2019 19:18:19: 24000000 INFO @ Sun, 02 Jun 2019 19:18:22: #1 tag size is determined as 67 bps INFO @ Sun, 02 Jun 2019 19:18:22: #1 tag size = 67 INFO @ Sun, 02 Jun 2019 19:18:22: #1 total tags in treatment: 24302917 INFO @ Sun, 02 Jun 2019 19:18:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:18:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:18:22: #1 tags after filtering in treatment: 24302917 INFO @ Sun, 02 Jun 2019 19:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:18:22: #1 finished! INFO @ Sun, 02 Jun 2019 19:18:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:18:24: #2 number of paired peaks: 142 WARNING @ Sun, 02 Jun 2019 19:18:24: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sun, 02 Jun 2019 19:18:24: start model_add_line... INFO @ Sun, 02 Jun 2019 19:18:24: start X-correlation... INFO @ Sun, 02 Jun 2019 19:18:24: end of X-cor INFO @ Sun, 02 Jun 2019 19:18:24: #2 finished! INFO @ Sun, 02 Jun 2019 19:18:24: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:18:24: #2 alternative fragment length(s) may be 1,25,44,60 bps INFO @ Sun, 02 Jun 2019 19:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.05_model.r WARNING @ Sun, 02 Jun 2019 19:18:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:18:24: #2 You may need to consider one of the other alternative d(s): 1,25,44,60 WARNING @ Sun, 02 Jun 2019 19:18:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:18:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:18:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:18:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.20_summits.bed INFO @ Sun, 02 Jun 2019 19:18:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.10_summits.bed INFO @ Sun, 02 Jun 2019 19:19:09: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:19:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194212/SRX4194212.05_summits.bed INFO @ Sun, 02 Jun 2019 19:19:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。