Job ID = 4288937 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:42:57 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 : 24,454,726 reads read : 48,909,452 reads written : 24,454,726 reads 0-length : 24,454,726 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:33:48 24454726 reads; of these: 24454726 (100.00%) were unpaired; of these: 4190787 (17.14%) aligned 0 times 16820050 (68.78%) aligned exactly 1 time 3443889 (14.08%) aligned >1 times 82.86% overall alignment rate Time searching: 00:33:54 Overall time: 00:33:54 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 12 files... [bam_rmdupse_core] 2274726 / 20263939 = 0.1123 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.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 13:43:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:29: 1000000 INFO @ Tue, 10 Dec 2019 13:43:38: 2000000 INFO @ Tue, 10 Dec 2019 13:43:48: 3000000 INFO @ Tue, 10 Dec 2019 13:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.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 13:43:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:57: 4000000 INFO @ Tue, 10 Dec 2019 13:43:58: 1000000 INFO @ Tue, 10 Dec 2019 13:44:07: 5000000 INFO @ Tue, 10 Dec 2019 13:44:07: 2000000 INFO @ Tue, 10 Dec 2019 13:44:16: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:44:16: 6000000 INFO @ Tue, 10 Dec 2019 13:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.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 13:44:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:44:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:44:25: 4000000 INFO @ Tue, 10 Dec 2019 13:44:26: 7000000 INFO @ Tue, 10 Dec 2019 13:44:28: 1000000 INFO @ Tue, 10 Dec 2019 13:44:33: 5000000 INFO @ Tue, 10 Dec 2019 13:44:36: 8000000 INFO @ Tue, 10 Dec 2019 13:44:37: 2000000 INFO @ Tue, 10 Dec 2019 13:44:42: 6000000 INFO @ Tue, 10 Dec 2019 13:44:45: 3000000 INFO @ Tue, 10 Dec 2019 13:44:46: 9000000 INFO @ Tue, 10 Dec 2019 13:44:51: 7000000 INFO @ Tue, 10 Dec 2019 13:44:54: 4000000 INFO @ Tue, 10 Dec 2019 13:44:55: 10000000 INFO @ Tue, 10 Dec 2019 13:45:00: 8000000 INFO @ Tue, 10 Dec 2019 13:45:02: 5000000 INFO @ Tue, 10 Dec 2019 13:45:05: 11000000 INFO @ Tue, 10 Dec 2019 13:45:09: 9000000 INFO @ Tue, 10 Dec 2019 13:45:11: 6000000 INFO @ Tue, 10 Dec 2019 13:45:15: 12000000 INFO @ Tue, 10 Dec 2019 13:45:18: 10000000 INFO @ Tue, 10 Dec 2019 13:45:19: 7000000 INFO @ Tue, 10 Dec 2019 13:45:25: 13000000 INFO @ Tue, 10 Dec 2019 13:45:27: 11000000 INFO @ Tue, 10 Dec 2019 13:45:28: 8000000 INFO @ Tue, 10 Dec 2019 13:45:35: 14000000 INFO @ Tue, 10 Dec 2019 13:45:36: 12000000 INFO @ Tue, 10 Dec 2019 13:45:36: 9000000 INFO @ Tue, 10 Dec 2019 13:45:45: 15000000 INFO @ Tue, 10 Dec 2019 13:45:45: 10000000 INFO @ Tue, 10 Dec 2019 13:45:45: 13000000 INFO @ Tue, 10 Dec 2019 13:45:53: 11000000 INFO @ Tue, 10 Dec 2019 13:45:54: 14000000 INFO @ Tue, 10 Dec 2019 13:45:55: 16000000 INFO @ Tue, 10 Dec 2019 13:46:02: 12000000 INFO @ Tue, 10 Dec 2019 13:46:03: 15000000 INFO @ Tue, 10 Dec 2019 13:46:04: 17000000 INFO @ Tue, 10 Dec 2019 13:46:10: 13000000 INFO @ Tue, 10 Dec 2019 13:46:13: 16000000 INFO @ Tue, 10 Dec 2019 13:46:15: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:46:15: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:46:15: #1 total tags in treatment: 17989213 INFO @ Tue, 10 Dec 2019 13:46:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:46:15: #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 13:46:15: #1 tags after filtering in treatment: 17988996 INFO @ Tue, 10 Dec 2019 13:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:46:15: #1 finished! INFO @ Tue, 10 Dec 2019 13:46:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:46:19: 14000000 INFO @ Tue, 10 Dec 2019 13:46:19: #2 number of paired peaks: 50274 INFO @ Tue, 10 Dec 2019 13:46:19: start model_add_line... INFO @ Tue, 10 Dec 2019 13:46:19: start X-correlation... INFO @ Tue, 10 Dec 2019 13:46:20: end of X-cor INFO @ Tue, 10 Dec 2019 13:46:20: #2 finished! INFO @ Tue, 10 Dec 2019 13:46:20: #2 predicted fragment length is 143 bps INFO @ Tue, 10 Dec 2019 13:46:20: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 10 Dec 2019 13:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.05_model.r WARNING @ Tue, 10 Dec 2019 13:46:20: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:46:20: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 10 Dec 2019 13:46:20: #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 13:46:20: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:46:22: 17000000 INFO @ Tue, 10 Dec 2019 13:46:27: 15000000 INFO @ Tue, 10 Dec 2019 13:46:31: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:46:31: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:46:31: #1 total tags in treatment: 17989213 INFO @ Tue, 10 Dec 2019 13:46:31: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:46:31: #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 13:46:31: #1 tags after filtering in treatment: 17988996 INFO @ Tue, 10 Dec 2019 13:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:46:31: #1 finished! INFO @ Tue, 10 Dec 2019 13:46:31: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:46:35: #2 number of paired peaks: 50274 INFO @ Tue, 10 Dec 2019 13:46:35: start model_add_line... INFO @ Tue, 10 Dec 2019 13:46:35: 16000000 INFO @ Tue, 10 Dec 2019 13:46:36: start X-correlation... INFO @ Tue, 10 Dec 2019 13:46:36: end of X-cor INFO @ Tue, 10 Dec 2019 13:46:36: #2 finished! INFO @ Tue, 10 Dec 2019 13:46:36: #2 predicted fragment length is 143 bps INFO @ Tue, 10 Dec 2019 13:46:36: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 10 Dec 2019 13:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.10_model.r WARNING @ Tue, 10 Dec 2019 13:46:36: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:46:36: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 10 Dec 2019 13:46:36: #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 13:46:36: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:46:44: 17000000 INFO @ Tue, 10 Dec 2019 13:46:52: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:46:52: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:46:52: #1 total tags in treatment: 17989213 INFO @ Tue, 10 Dec 2019 13:46:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:46:52: #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 13:46:53: #1 tags after filtering in treatment: 17988996 INFO @ Tue, 10 Dec 2019 13:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:46:53: #1 finished! INFO @ Tue, 10 Dec 2019 13:46:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:46:57: #2 number of paired peaks: 50274 INFO @ Tue, 10 Dec 2019 13:46:57: start model_add_line... INFO @ Tue, 10 Dec 2019 13:46:57: start X-correlation... INFO @ Tue, 10 Dec 2019 13:46:57: end of X-cor INFO @ Tue, 10 Dec 2019 13:46:57: #2 finished! INFO @ Tue, 10 Dec 2019 13:46:57: #2 predicted fragment length is 143 bps INFO @ Tue, 10 Dec 2019 13:46:57: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 10 Dec 2019 13:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.20_model.r WARNING @ Tue, 10 Dec 2019 13:46:57: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:46:57: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 10 Dec 2019 13:46:57: #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 13:46:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:47:20: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:47:37: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:47:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:47:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.05_summits.bed INFO @ Tue, 10 Dec 2019 13:47:51: Done! pass1 - making usageList (78 chroms): 3 millis pass2 - checking and writing primary data (11702 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:47:56: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.10_summits.bed INFO @ Tue, 10 Dec 2019 13:48:10: Done! pass1 - making usageList (57 chroms): 4 millis pass2 - checking and writing primary data (7423 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460571/SRX5460571.20_summits.bed INFO @ Tue, 10 Dec 2019 13:48:28: Done! pass1 - making usageList (38 chroms): 3 millis pass2 - checking and writing primary data (2961 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。