Job ID = 1292402 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,493,038 reads read : 14,986,076 reads written : 7,493,038 reads 0-length : 7,493,038 2019-06-02T09:20:33 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' 2019-06-02T09:20:33 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/SRR7291438' 2019-06-02T09:20:33 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291438' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:20:33 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 7,336,373 reads read : 14,672,746 reads written : 7,336,373 reads 0-length : 7,336,373 spots read : 7,480,446 reads read : 14,960,892 reads written : 7,480,446 reads 0-length : 7,480,446 spots read : 7,251,348 reads read : 14,502,696 reads written : 7,251,348 reads 0-length : 7,251,348 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: 00:14:07 29561205 reads; of these: 29561205 (100.00%) were unpaired; of these: 650195 (2.20%) aligned 0 times 20734417 (70.14%) aligned exactly 1 time 8176593 (27.66%) aligned >1 times 97.80% overall alignment rate Time searching: 00:14:07 Overall time: 00:14:07 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 12 files... [bam_rmdupse_core] 10623618 / 28911010 = 0.3675 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 19:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.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 19:02:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:02:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.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 19:02:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:02:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.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 19:02:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:02:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:02:54: 1000000 INFO @ Sun, 02 Jun 2019 19:02:55: 1000000 INFO @ Sun, 02 Jun 2019 19:02:56: 1000000 INFO @ Sun, 02 Jun 2019 19:03:04: 2000000 INFO @ Sun, 02 Jun 2019 19:03:04: 2000000 INFO @ Sun, 02 Jun 2019 19:03:07: 2000000 INFO @ Sun, 02 Jun 2019 19:03:14: 3000000 INFO @ Sun, 02 Jun 2019 19:03:14: 3000000 INFO @ Sun, 02 Jun 2019 19:03:17: 3000000 INFO @ Sun, 02 Jun 2019 19:03:23: 4000000 INFO @ Sun, 02 Jun 2019 19:03:23: 4000000 INFO @ Sun, 02 Jun 2019 19:03:28: 4000000 INFO @ Sun, 02 Jun 2019 19:03:33: 5000000 INFO @ Sun, 02 Jun 2019 19:03:33: 5000000 INFO @ Sun, 02 Jun 2019 19:03:38: 5000000 INFO @ Sun, 02 Jun 2019 19:03:42: 6000000 INFO @ Sun, 02 Jun 2019 19:03:43: 6000000 INFO @ Sun, 02 Jun 2019 19:03:49: 6000000 INFO @ Sun, 02 Jun 2019 19:03:52: 7000000 INFO @ Sun, 02 Jun 2019 19:03:52: 7000000 INFO @ Sun, 02 Jun 2019 19:03:59: 7000000 INFO @ Sun, 02 Jun 2019 19:04:02: 8000000 INFO @ Sun, 02 Jun 2019 19:04:02: 8000000 INFO @ Sun, 02 Jun 2019 19:04:09: 8000000 INFO @ Sun, 02 Jun 2019 19:04:12: 9000000 INFO @ Sun, 02 Jun 2019 19:04:12: 9000000 INFO @ Sun, 02 Jun 2019 19:04:21: 9000000 INFO @ Sun, 02 Jun 2019 19:04:22: 10000000 INFO @ Sun, 02 Jun 2019 19:04:22: 10000000 INFO @ Sun, 02 Jun 2019 19:04:31: 10000000 INFO @ Sun, 02 Jun 2019 19:04:32: 11000000 INFO @ Sun, 02 Jun 2019 19:04:32: 11000000 INFO @ Sun, 02 Jun 2019 19:04:41: 12000000 INFO @ Sun, 02 Jun 2019 19:04:42: 12000000 INFO @ Sun, 02 Jun 2019 19:04:42: 11000000 INFO @ Sun, 02 Jun 2019 19:04:52: 13000000 INFO @ Sun, 02 Jun 2019 19:04:52: 13000000 INFO @ Sun, 02 Jun 2019 19:04:52: 12000000 INFO @ Sun, 02 Jun 2019 19:05:01: 14000000 INFO @ Sun, 02 Jun 2019 19:05:02: 14000000 INFO @ Sun, 02 Jun 2019 19:05:03: 13000000 INFO @ Sun, 02 Jun 2019 19:05:11: 15000000 INFO @ Sun, 02 Jun 2019 19:05:11: 15000000 INFO @ Sun, 02 Jun 2019 19:05:13: 14000000 INFO @ Sun, 02 Jun 2019 19:05:20: 16000000 INFO @ Sun, 02 Jun 2019 19:05:21: 16000000 INFO @ Sun, 02 Jun 2019 19:05:24: 15000000 INFO @ Sun, 02 Jun 2019 19:05:29: 17000000 INFO @ Sun, 02 Jun 2019 19:05:30: 17000000 INFO @ Sun, 02 Jun 2019 19:05:35: 16000000 INFO @ Sun, 02 Jun 2019 19:05:38: 18000000 INFO @ Sun, 02 Jun 2019 19:05:39: 18000000 INFO @ Sun, 02 Jun 2019 19:05:41: #1 tag size is determined as 58 bps INFO @ Sun, 02 Jun 2019 19:05:41: #1 tag size = 58 INFO @ Sun, 02 Jun 2019 19:05:41: #1 total tags in treatment: 18287392 INFO @ Sun, 02 Jun 2019 19:05:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:05:41: #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 19:05:41: #1 tags after filtering in treatment: 18287392 INFO @ Sun, 02 Jun 2019 19:05:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:05:41: #1 finished! INFO @ Sun, 02 Jun 2019 19:05:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:05:42: #1 tag size is determined as 58 bps INFO @ Sun, 02 Jun 2019 19:05:42: #1 tag size = 58 INFO @ Sun, 02 Jun 2019 19:05:42: #1 total tags in treatment: 18287392 INFO @ Sun, 02 Jun 2019 19:05:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:05:42: #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 19:05:42: #1 tags after filtering in treatment: 18287392 INFO @ Sun, 02 Jun 2019 19:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:05:42: #1 finished! INFO @ Sun, 02 Jun 2019 19:05:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:05:43: #2 number of paired peaks: 658 WARNING @ Sun, 02 Jun 2019 19:05:43: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Sun, 02 Jun 2019 19:05:43: start model_add_line... INFO @ Sun, 02 Jun 2019 19:05:43: start X-correlation... INFO @ Sun, 02 Jun 2019 19:05:43: end of X-cor INFO @ Sun, 02 Jun 2019 19:05:43: #2 finished! INFO @ Sun, 02 Jun 2019 19:05:43: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:05:43: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 02 Jun 2019 19:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.05_model.r WARNING @ Sun, 02 Jun 2019 19:05:43: #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 19:05:43: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 02 Jun 2019 19:05:43: #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 19:05:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:05:44: #2 number of paired peaks: 658 WARNING @ Sun, 02 Jun 2019 19:05:44: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Sun, 02 Jun 2019 19:05:44: start model_add_line... INFO @ Sun, 02 Jun 2019 19:05:44: start X-correlation... INFO @ Sun, 02 Jun 2019 19:05:44: end of X-cor INFO @ Sun, 02 Jun 2019 19:05:44: #2 finished! INFO @ Sun, 02 Jun 2019 19:05:44: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:05:44: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 02 Jun 2019 19:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.20_model.r WARNING @ Sun, 02 Jun 2019 19:05:44: #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 19:05:44: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 02 Jun 2019 19:05:44: #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 19:05:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:05:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:05:45: 17000000 INFO @ Sun, 02 Jun 2019 19:05:55: 18000000 INFO @ Sun, 02 Jun 2019 19:05:58: #1 tag size is determined as 58 bps INFO @ Sun, 02 Jun 2019 19:05:58: #1 tag size = 58 INFO @ Sun, 02 Jun 2019 19:05:58: #1 total tags in treatment: 18287392 INFO @ Sun, 02 Jun 2019 19:05:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:05:58: #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 19:05:59: #1 tags after filtering in treatment: 18287392 INFO @ Sun, 02 Jun 2019 19:05:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:05:59: #1 finished! INFO @ Sun, 02 Jun 2019 19:05:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:06:00: #2 number of paired peaks: 658 WARNING @ Sun, 02 Jun 2019 19:06:00: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Sun, 02 Jun 2019 19:06:00: start model_add_line... INFO @ Sun, 02 Jun 2019 19:06:00: start X-correlation... INFO @ Sun, 02 Jun 2019 19:06:00: end of X-cor INFO @ Sun, 02 Jun 2019 19:06:00: #2 finished! INFO @ Sun, 02 Jun 2019 19:06:00: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:06:00: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 02 Jun 2019 19:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.10_model.r WARNING @ Sun, 02 Jun 2019 19:06:00: #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 19:06:00: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 02 Jun 2019 19:06:00: #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 19:06:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:06:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:06:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.05_summits.bed INFO @ Sun, 02 Jun 2019 19:06:39: Done! INFO @ Sun, 02 Jun 2019 19:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.20_summits.bed INFO @ Sun, 02 Jun 2019 19:06:39: Done! pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194184/SRX4194184.10_summits.bed INFO @ Sun, 02 Jun 2019 19:06:56: Done! pass1 - making usageList (0 chroms): 2 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。