Job ID = 1292406 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,888,993 reads read : 9,777,986 reads written : 4,888,993 reads 0-length : 4,888,993 2019-06-02T09:20:48 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' 2019-06-02T09:20:48 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/SRR7291451' 2019-06-02T09:20:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291451' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:20:48 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 4,764,869 reads read : 9,529,738 reads written : 4,764,869 reads 0-length : 4,764,869 spots read : 4,871,183 reads read : 9,742,366 reads written : 4,871,183 reads 0-length : 4,871,183 2019-06-02T09:30:52 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' 2019-06-02T09:30:52 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/SRR7291453' 2019-06-02T09:30:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291453' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:30:52 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 4,726,826 reads read : 9,453,652 reads written : 4,726,826 reads 0-length : 4,726,826 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: 00:09:03 19251871 reads; of these: 19251871 (100.00%) were unpaired; of these: 449341 (2.33%) aligned 0 times 13948559 (72.45%) aligned exactly 1 time 4853971 (25.21%) aligned >1 times 97.67% overall alignment rate Time searching: 00:09:03 Overall time: 00:09:03 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 8 files... [bam_rmdupse_core] 6291718 / 18802530 = 0.3346 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 18:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.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 18:52:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:52:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.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 18:52:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:52:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.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 18:52:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:52:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:52:55: 1000000 INFO @ Sun, 02 Jun 2019 18:52:55: 1000000 INFO @ Sun, 02 Jun 2019 18:52:56: 1000000 INFO @ Sun, 02 Jun 2019 18:53:03: 2000000 INFO @ Sun, 02 Jun 2019 18:53:05: 2000000 INFO @ Sun, 02 Jun 2019 18:53:07: 2000000 INFO @ Sun, 02 Jun 2019 18:53:12: 3000000 INFO @ Sun, 02 Jun 2019 18:53:15: 3000000 INFO @ Sun, 02 Jun 2019 18:53:18: 3000000 INFO @ Sun, 02 Jun 2019 18:53:20: 4000000 INFO @ Sun, 02 Jun 2019 18:53:26: 4000000 INFO @ Sun, 02 Jun 2019 18:53:28: 4000000 INFO @ Sun, 02 Jun 2019 18:53:29: 5000000 INFO @ Sun, 02 Jun 2019 18:53:37: 6000000 INFO @ Sun, 02 Jun 2019 18:53:37: 5000000 INFO @ Sun, 02 Jun 2019 18:53:40: 5000000 INFO @ Sun, 02 Jun 2019 18:53:45: 7000000 INFO @ Sun, 02 Jun 2019 18:53:47: 6000000 INFO @ Sun, 02 Jun 2019 18:53:50: 6000000 INFO @ Sun, 02 Jun 2019 18:53:53: 8000000 INFO @ Sun, 02 Jun 2019 18:53:58: 7000000 INFO @ Sun, 02 Jun 2019 18:54:01: 7000000 INFO @ Sun, 02 Jun 2019 18:54:01: 9000000 INFO @ Sun, 02 Jun 2019 18:54:08: 8000000 INFO @ Sun, 02 Jun 2019 18:54:10: 10000000 INFO @ Sun, 02 Jun 2019 18:54:12: 8000000 INFO @ Sun, 02 Jun 2019 18:54:18: 11000000 INFO @ Sun, 02 Jun 2019 18:54:19: 9000000 INFO @ Sun, 02 Jun 2019 18:54:22: 9000000 INFO @ Sun, 02 Jun 2019 18:54:26: 12000000 INFO @ Sun, 02 Jun 2019 18:54:29: 10000000 INFO @ Sun, 02 Jun 2019 18:54:30: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 18:54:30: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 18:54:30: #1 total tags in treatment: 12510812 INFO @ Sun, 02 Jun 2019 18:54:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:54:30: #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 18:54:30: #1 tags after filtering in treatment: 12510812 INFO @ Sun, 02 Jun 2019 18:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:54:30: #1 finished! INFO @ Sun, 02 Jun 2019 18:54:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:54:32: #2 number of paired peaks: 603 WARNING @ Sun, 02 Jun 2019 18:54:32: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 02 Jun 2019 18:54:32: start model_add_line... INFO @ Sun, 02 Jun 2019 18:54:32: start X-correlation... INFO @ Sun, 02 Jun 2019 18:54:32: end of X-cor INFO @ Sun, 02 Jun 2019 18:54:32: #2 finished! INFO @ Sun, 02 Jun 2019 18:54:32: #2 predicted fragment length is 59 bps INFO @ Sun, 02 Jun 2019 18:54:32: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 02 Jun 2019 18:54:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.05_model.r WARNING @ Sun, 02 Jun 2019 18:54:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:54:32: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 02 Jun 2019 18:54:32: #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 18:54:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:54:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:54:33: 10000000 INFO @ Sun, 02 Jun 2019 18:54:39: 11000000 INFO @ Sun, 02 Jun 2019 18:54:43: 11000000 INFO @ Sun, 02 Jun 2019 18:54:50: 12000000 INFO @ Sun, 02 Jun 2019 18:54:54: 12000000 INFO @ Sun, 02 Jun 2019 18:54:55: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 18:54:55: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 18:54:55: #1 total tags in treatment: 12510812 INFO @ Sun, 02 Jun 2019 18:54:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:54:55: #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 18:54:55: #1 tags after filtering in treatment: 12510812 INFO @ Sun, 02 Jun 2019 18:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:54:55: #1 finished! INFO @ Sun, 02 Jun 2019 18:54:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:54:56: #2 number of paired peaks: 603 WARNING @ Sun, 02 Jun 2019 18:54:56: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 02 Jun 2019 18:54:56: start model_add_line... INFO @ Sun, 02 Jun 2019 18:54:56: start X-correlation... INFO @ Sun, 02 Jun 2019 18:54:56: end of X-cor INFO @ Sun, 02 Jun 2019 18:54:56: #2 finished! INFO @ Sun, 02 Jun 2019 18:54:56: #2 predicted fragment length is 59 bps INFO @ Sun, 02 Jun 2019 18:54:56: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 02 Jun 2019 18:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.20_model.r WARNING @ Sun, 02 Jun 2019 18:54:56: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:54:56: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 02 Jun 2019 18:54:56: #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 18:54:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:54:59: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 18:54:59: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 18:54:59: #1 total tags in treatment: 12510812 INFO @ Sun, 02 Jun 2019 18:54:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:54:59: #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 18:54:59: #1 tags after filtering in treatment: 12510812 INFO @ Sun, 02 Jun 2019 18:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:54:59: #1 finished! INFO @ Sun, 02 Jun 2019 18:54:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:00: #2 number of paired peaks: 603 WARNING @ Sun, 02 Jun 2019 18:55:00: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 02 Jun 2019 18:55:00: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:00: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:00: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:00: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:00: #2 predicted fragment length is 59 bps INFO @ Sun, 02 Jun 2019 18:55:00: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 02 Jun 2019 18:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.10_model.r WARNING @ Sun, 02 Jun 2019 18:55:00: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:55:00: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 02 Jun 2019 18:55:00: #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 18:55:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.05_summits.bed INFO @ Sun, 02 Jun 2019 18:55:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1798 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:55:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:55:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.20_summits.bed INFO @ Sun, 02 Jun 2019 18:55:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194188/SRX4194188.10_summits.bed INFO @ Sun, 02 Jun 2019 18:55:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (763 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。