Job ID = 4288915 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:35:39 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 ) 2019-12-10T03:39:52 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 : 17,014,863 reads read : 34,029,726 reads written : 17,014,863 reads 0-length : 17,014,863 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:19:35 17014863 reads; of these: 17014863 (100.00%) were unpaired; of these: 1509964 (8.87%) aligned 0 times 12922576 (75.95%) aligned exactly 1 time 2582323 (15.18%) aligned >1 times 91.13% overall alignment rate Time searching: 00:19:41 Overall time: 00:19:41 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] 4642499 / 15504899 = 0.2994 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:11:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.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 @ Tue, 10 Dec 2019 13:11:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:11:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:12:01: 1000000 INFO @ Tue, 10 Dec 2019 13:12:14: 2000000 INFO @ Tue, 10 Dec 2019 13:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.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 @ Tue, 10 Dec 2019 13:12:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:12:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:12:26: 1000000 INFO @ Tue, 10 Dec 2019 13:12:28: 3000000 INFO @ Tue, 10 Dec 2019 13:12:36: 2000000 INFO @ Tue, 10 Dec 2019 13:12:42: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:12:46: 3000000 INFO @ Tue, 10 Dec 2019 13:12:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.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 @ Tue, 10 Dec 2019 13:12:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:12:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:12:56: 4000000 INFO @ Tue, 10 Dec 2019 13:12:57: 5000000 INFO @ Tue, 10 Dec 2019 13:12:58: 1000000 INFO @ Tue, 10 Dec 2019 13:13:06: 5000000 INFO @ Tue, 10 Dec 2019 13:13:10: 2000000 INFO @ Tue, 10 Dec 2019 13:13:11: 6000000 INFO @ Tue, 10 Dec 2019 13:13:16: 6000000 INFO @ Tue, 10 Dec 2019 13:13:21: 3000000 INFO @ Tue, 10 Dec 2019 13:13:25: 7000000 INFO @ Tue, 10 Dec 2019 13:13:26: 7000000 INFO @ Tue, 10 Dec 2019 13:13:33: 4000000 INFO @ Tue, 10 Dec 2019 13:13:36: 8000000 INFO @ Tue, 10 Dec 2019 13:13:40: 8000000 INFO @ Tue, 10 Dec 2019 13:13:44: 5000000 INFO @ Tue, 10 Dec 2019 13:13:45: 9000000 INFO @ Tue, 10 Dec 2019 13:13:53: 9000000 INFO @ Tue, 10 Dec 2019 13:13:55: 10000000 INFO @ Tue, 10 Dec 2019 13:13:57: 6000000 INFO @ Tue, 10 Dec 2019 13:14:04: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:14:04: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:14:04: #1 total tags in treatment: 10862400 INFO @ Tue, 10 Dec 2019 13:14:04: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:14:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:14:04: #1 tags after filtering in treatment: 10862191 INFO @ Tue, 10 Dec 2019 13:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:14:04: #1 finished! INFO @ Tue, 10 Dec 2019 13:14:04: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:14:06: 10000000 INFO @ Tue, 10 Dec 2019 13:14:08: #2 number of paired peaks: 59577 INFO @ Tue, 10 Dec 2019 13:14:08: start model_add_line... INFO @ Tue, 10 Dec 2019 13:14:08: start X-correlation... INFO @ Tue, 10 Dec 2019 13:14:08: end of X-cor INFO @ Tue, 10 Dec 2019 13:14:08: #2 finished! INFO @ Tue, 10 Dec 2019 13:14:08: #2 predicted fragment length is 164 bps INFO @ Tue, 10 Dec 2019 13:14:08: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 10 Dec 2019 13:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.10_model.r WARNING @ Tue, 10 Dec 2019 13:14:08: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:14:08: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Tue, 10 Dec 2019 13:14:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:14:08: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:14:09: 7000000 INFO @ Tue, 10 Dec 2019 13:14:18: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:14:18: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:14:18: #1 total tags in treatment: 10862400 INFO @ Tue, 10 Dec 2019 13:14:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:14:18: #1 tags after filtering in treatment: 10862191 INFO @ Tue, 10 Dec 2019 13:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:14:18: #1 finished! INFO @ Tue, 10 Dec 2019 13:14:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:14:20: 8000000 INFO @ Tue, 10 Dec 2019 13:14:22: #2 number of paired peaks: 59577 INFO @ Tue, 10 Dec 2019 13:14:22: start model_add_line... INFO @ Tue, 10 Dec 2019 13:14:22: start X-correlation... INFO @ Tue, 10 Dec 2019 13:14:22: end of X-cor INFO @ Tue, 10 Dec 2019 13:14:22: #2 finished! INFO @ Tue, 10 Dec 2019 13:14:22: #2 predicted fragment length is 164 bps INFO @ Tue, 10 Dec 2019 13:14:22: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 10 Dec 2019 13:14:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.05_model.r WARNING @ Tue, 10 Dec 2019 13:14:22: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:14:22: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Tue, 10 Dec 2019 13:14:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:14:22: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:14:33: 9000000 INFO @ Tue, 10 Dec 2019 13:14:43: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:14:46: 10000000 INFO @ Tue, 10 Dec 2019 13:14:56: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:14:56: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:14:56: #1 total tags in treatment: 10862400 INFO @ Tue, 10 Dec 2019 13:14:56: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:14:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:14:56: #1 tags after filtering in treatment: 10862191 INFO @ Tue, 10 Dec 2019 13:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:14:56: #1 finished! INFO @ Tue, 10 Dec 2019 13:14:56: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:14:58: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:14:59: #2 number of paired peaks: 59577 INFO @ Tue, 10 Dec 2019 13:14:59: start model_add_line... INFO @ Tue, 10 Dec 2019 13:15:00: start X-correlation... INFO @ Tue, 10 Dec 2019 13:15:00: end of X-cor INFO @ Tue, 10 Dec 2019 13:15:00: #2 finished! INFO @ Tue, 10 Dec 2019 13:15:00: #2 predicted fragment length is 164 bps INFO @ Tue, 10 Dec 2019 13:15:00: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 10 Dec 2019 13:15:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.20_model.r WARNING @ Tue, 10 Dec 2019 13:15:00: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:15:00: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Tue, 10 Dec 2019 13:15:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:15:00: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:15:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.10_summits.bed INFO @ Tue, 10 Dec 2019 13:15:02: Done! pass1 - making usageList (62 chroms): 7 millis pass2 - checking and writing primary data (16777 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.05_summits.bed INFO @ Tue, 10 Dec 2019 13:15:17: Done! pass1 - making usageList (100 chroms): 12 millis pass2 - checking and writing primary data (34200 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:15:36: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460563/SRX5460563.20_summits.bed INFO @ Tue, 10 Dec 2019 13:15:56: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (6288 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。