Job ID = 1292385 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T09:13:30 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 ) 2019-06-02T09:13:30 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 : 71,485,065 reads read : 142,970,130 reads written : 71,485,065 reads 0-length : 71,485,065 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:15:42 71485065 reads; of these: 71485065 (100.00%) were unpaired; of these: 10099631 (14.13%) aligned 0 times 52458913 (73.38%) aligned exactly 1 time 8926521 (12.49%) aligned >1 times 85.87% overall alignment rate Time searching: 00:15:42 Overall time: 00:15:42 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 28 files... [bam_rmdupse_core] 56639914 / 61385434 = 0.9227 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 18:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.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 18:55:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.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 18:55:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.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 18:55:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:20: 1000000 INFO @ Sun, 02 Jun 2019 18:55:22: 1000000 INFO @ Sun, 02 Jun 2019 18:55:24: 1000000 INFO @ Sun, 02 Jun 2019 18:55:30: 2000000 INFO @ Sun, 02 Jun 2019 18:55:35: 2000000 INFO @ Sun, 02 Jun 2019 18:55:37: 2000000 INFO @ Sun, 02 Jun 2019 18:55:39: 3000000 INFO @ Sun, 02 Jun 2019 18:55:48: 3000000 INFO @ Sun, 02 Jun 2019 18:55:50: 4000000 INFO @ Sun, 02 Jun 2019 18:55:52: 3000000 INFO @ Sun, 02 Jun 2019 18:55:57: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:55:57: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:55:57: #1 total tags in treatment: 4745520 INFO @ Sun, 02 Jun 2019 18:55:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:57: #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 18:55:57: #1 tags after filtering in treatment: 4745520 INFO @ Sun, 02 Jun 2019 18:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:57: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:58: #2 number of paired peaks: 1418 INFO @ Sun, 02 Jun 2019 18:55:58: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:58: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:58: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:58: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:58: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 18:55:58: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 02 Jun 2019 18:55:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.20_model.r WARNING @ Sun, 02 Jun 2019 18:55:58: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:55:58: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 02 Jun 2019 18:55:58: #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 18:55:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:02: 4000000 INFO @ Sun, 02 Jun 2019 18:56:06: 4000000 INFO @ Sun, 02 Jun 2019 18:56:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:56:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:56:11: #1 total tags in treatment: 4745520 INFO @ Sun, 02 Jun 2019 18:56:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:11: #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 18:56:11: #1 tags after filtering in treatment: 4745520 INFO @ Sun, 02 Jun 2019 18:56:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:11: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:12: #2 number of paired peaks: 1418 INFO @ Sun, 02 Jun 2019 18:56:12: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:12: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:12: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:12: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:12: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 18:56:12: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 02 Jun 2019 18:56:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.05_model.r WARNING @ Sun, 02 Jun 2019 18:56:12: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:12: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 02 Jun 2019 18:56:12: #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 18:56:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:56:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:56:15: #1 total tags in treatment: 4745520 INFO @ Sun, 02 Jun 2019 18:56:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:15: #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 18:56:15: #1 tags after filtering in treatment: 4745520 INFO @ Sun, 02 Jun 2019 18:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:15: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:16: #2 number of paired peaks: 1418 INFO @ Sun, 02 Jun 2019 18:56:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:16: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 18:56:16: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sun, 02 Jun 2019 18:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.10_model.r WARNING @ Sun, 02 Jun 2019 18:56:16: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:16: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sun, 02 Jun 2019 18:56:16: #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 18:56:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.20_summits.bed INFO @ Sun, 02 Jun 2019 18:56:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:56:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.05_summits.bed INFO @ Sun, 02 Jun 2019 18:56:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3265 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923762/SRX3923762.10_summits.bed INFO @ Sun, 02 Jun 2019 18:56:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1170 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。