Job ID = 4288933 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,906,753 reads read : 21,813,506 reads written : 10,906,753 reads 0-length : 10,906,753 2019-12-10T03:51:17 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 ) 2019-12-10T03:51:17 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 : 12,703,099 reads read : 25,406,198 reads written : 12,703,099 reads 0-length : 12,703,099 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:25:28 23609852 reads; of these: 23609852 (100.00%) were unpaired; of these: 4872742 (20.64%) aligned 0 times 15400333 (65.23%) aligned exactly 1 time 3336777 (14.13%) aligned >1 times 79.36% overall alignment rate Time searching: 00:25:31 Overall time: 00:25:31 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] 2268011 / 18737110 = 0.1210 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.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 13:32:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:32:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:32:59: 1000000 INFO @ Tue, 10 Dec 2019 13:33:10: 2000000 INFO @ Tue, 10 Dec 2019 13:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.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 13:33:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:33:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:33:20: 3000000 INFO @ Tue, 10 Dec 2019 13:33:28: 1000000 INFO @ Tue, 10 Dec 2019 13:33:31: 4000000 INFO @ Tue, 10 Dec 2019 13:33:38: 2000000 INFO @ Tue, 10 Dec 2019 13:33:42: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:33:47: 3000000 INFO @ Tue, 10 Dec 2019 13:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.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 13:33:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:33:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:33:53: 6000000 INFO @ Tue, 10 Dec 2019 13:33:59: 4000000 INFO @ Tue, 10 Dec 2019 13:34:00: 1000000 INFO @ Tue, 10 Dec 2019 13:34:05: 7000000 INFO @ Tue, 10 Dec 2019 13:34:10: 5000000 INFO @ Tue, 10 Dec 2019 13:34:12: 2000000 INFO @ Tue, 10 Dec 2019 13:34:16: 8000000 INFO @ Tue, 10 Dec 2019 13:34:22: 6000000 INFO @ Tue, 10 Dec 2019 13:34:23: 3000000 INFO @ Tue, 10 Dec 2019 13:34:27: 9000000 INFO @ Tue, 10 Dec 2019 13:34:33: 7000000 INFO @ Tue, 10 Dec 2019 13:34:35: 4000000 INFO @ Tue, 10 Dec 2019 13:34:39: 10000000 INFO @ Tue, 10 Dec 2019 13:34:45: 8000000 INFO @ Tue, 10 Dec 2019 13:34:46: 5000000 INFO @ Tue, 10 Dec 2019 13:34:50: 11000000 INFO @ Tue, 10 Dec 2019 13:34:56: 9000000 INFO @ Tue, 10 Dec 2019 13:34:58: 6000000 INFO @ Tue, 10 Dec 2019 13:35:01: 12000000 INFO @ Tue, 10 Dec 2019 13:35:08: 10000000 INFO @ Tue, 10 Dec 2019 13:35:09: 7000000 INFO @ Tue, 10 Dec 2019 13:35:13: 13000000 INFO @ Tue, 10 Dec 2019 13:35:19: 11000000 INFO @ Tue, 10 Dec 2019 13:35:20: 8000000 INFO @ Tue, 10 Dec 2019 13:35:24: 14000000 INFO @ Tue, 10 Dec 2019 13:35:31: 12000000 INFO @ Tue, 10 Dec 2019 13:35:32: 9000000 INFO @ Tue, 10 Dec 2019 13:35:36: 15000000 INFO @ Tue, 10 Dec 2019 13:35:42: 13000000 INFO @ Tue, 10 Dec 2019 13:35:44: 10000000 INFO @ Tue, 10 Dec 2019 13:35:47: 16000000 INFO @ Tue, 10 Dec 2019 13:35:52: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:35:52: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:35:52: #1 total tags in treatment: 16469099 INFO @ Tue, 10 Dec 2019 13:35:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:35:52: #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 13:35:53: #1 tags after filtering in treatment: 16468905 INFO @ Tue, 10 Dec 2019 13:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:35:53: #1 finished! INFO @ Tue, 10 Dec 2019 13:35:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:35:54: 14000000 INFO @ Tue, 10 Dec 2019 13:35:55: 11000000 INFO @ Tue, 10 Dec 2019 13:35:57: #2 number of paired peaks: 56124 INFO @ Tue, 10 Dec 2019 13:35:57: start model_add_line... INFO @ Tue, 10 Dec 2019 13:35:57: start X-correlation... INFO @ Tue, 10 Dec 2019 13:35:57: end of X-cor INFO @ Tue, 10 Dec 2019 13:35:57: #2 finished! INFO @ Tue, 10 Dec 2019 13:35:57: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:35:57: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 10 Dec 2019 13:35:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.05_model.r WARNING @ Tue, 10 Dec 2019 13:35:57: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:35:57: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Tue, 10 Dec 2019 13:35:57: #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 13:35:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:36:05: 15000000 INFO @ Tue, 10 Dec 2019 13:36:06: 12000000 INFO @ Tue, 10 Dec 2019 13:36:16: 16000000 INFO @ Tue, 10 Dec 2019 13:36:17: 13000000 INFO @ Tue, 10 Dec 2019 13:36:21: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:36:21: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:36:21: #1 total tags in treatment: 16469099 INFO @ Tue, 10 Dec 2019 13:36:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:36:21: #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 13:36:21: #1 tags after filtering in treatment: 16468905 INFO @ Tue, 10 Dec 2019 13:36:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:36:21: #1 finished! INFO @ Tue, 10 Dec 2019 13:36:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:36:25: #2 number of paired peaks: 56124 INFO @ Tue, 10 Dec 2019 13:36:25: start model_add_line... INFO @ Tue, 10 Dec 2019 13:36:25: start X-correlation... INFO @ Tue, 10 Dec 2019 13:36:25: end of X-cor INFO @ Tue, 10 Dec 2019 13:36:25: #2 finished! INFO @ Tue, 10 Dec 2019 13:36:25: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:36:25: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 10 Dec 2019 13:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.10_model.r WARNING @ Tue, 10 Dec 2019 13:36:25: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:36:25: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Tue, 10 Dec 2019 13:36:25: #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 13:36:25: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:36:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:36:27: 14000000 INFO @ Tue, 10 Dec 2019 13:36:36: 15000000 INFO @ Tue, 10 Dec 2019 13:36:45: 16000000 INFO @ Tue, 10 Dec 2019 13:36:50: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:36:50: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:36:50: #1 total tags in treatment: 16469099 INFO @ Tue, 10 Dec 2019 13:36:50: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:36:50: #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 13:36:50: #1 tags after filtering in treatment: 16468905 INFO @ Tue, 10 Dec 2019 13:36:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:36:50: #1 finished! INFO @ Tue, 10 Dec 2019 13:36:50: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:36:51: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:36:54: #2 number of paired peaks: 56124 INFO @ Tue, 10 Dec 2019 13:36:54: start model_add_line... INFO @ Tue, 10 Dec 2019 13:36:54: start X-correlation... INFO @ Tue, 10 Dec 2019 13:36:54: end of X-cor INFO @ Tue, 10 Dec 2019 13:36:54: #2 finished! INFO @ Tue, 10 Dec 2019 13:36:54: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:36:54: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 10 Dec 2019 13:36:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.20_model.r WARNING @ Tue, 10 Dec 2019 13:36:54: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:36:54: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Tue, 10 Dec 2019 13:36:54: #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 13:36:54: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.05_summits.bed INFO @ Tue, 10 Dec 2019 13:37:18: Done! pass1 - making usageList (66 chroms): 6 millis pass2 - checking and writing primary data (8793 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:37:20: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:37:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.10_summits.bed INFO @ Tue, 10 Dec 2019 13:37:46: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (4352 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:37:48: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460570/SRX5460570.20_summits.bed INFO @ Tue, 10 Dec 2019 13:38:15: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (1222 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。