Job ID = 4288952 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:49:06 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 ) 2019-12-10T03:49:06 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 : 11,175,825 reads read : 22,351,650 reads written : 11,175,825 reads 0-length : 11,175,825 2019-12-10T03:54:54 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 ) 2019-12-10T03:54:54 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 ) 2019-12-10T03:54:54 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 ) 2019-12-10T03:54:55 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 ) 2019-12-10T03:54:55 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 ) 2019-12-10T03:54:55 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 : 11,663,274 reads read : 23,326,548 reads written : 11,663,274 reads 0-length : 11,663,274 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: 00:32:10 22839099 reads; of these: 22839099 (100.00%) were unpaired; of these: 927179 (4.06%) aligned 0 times 16366798 (71.66%) aligned exactly 1 time 5545122 (24.28%) aligned >1 times 95.94% overall alignment rate Time searching: 00:32:12 Overall time: 00:32:12 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] 1855772 / 21911920 = 0.0847 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.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 13:47:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:47:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:47:42: 1000000 INFO @ Tue, 10 Dec 2019 13:47:52: 2000000 INFO @ Tue, 10 Dec 2019 13:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.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 13:48:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:48:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:48:03: 3000000 INFO @ Tue, 10 Dec 2019 13:48:13: 1000000 INFO @ Tue, 10 Dec 2019 13:48:14: 4000000 INFO @ Tue, 10 Dec 2019 13:48:23: 2000000 INFO @ Tue, 10 Dec 2019 13:48:24: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.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 13:48:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:48:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:48:35: 3000000 INFO @ Tue, 10 Dec 2019 13:48:36: 6000000 INFO @ Tue, 10 Dec 2019 13:48:42: 1000000 INFO @ Tue, 10 Dec 2019 13:48:46: 4000000 INFO @ Tue, 10 Dec 2019 13:48:48: 7000000 INFO @ Tue, 10 Dec 2019 13:48:52: 2000000 INFO @ Tue, 10 Dec 2019 13:48:56: 5000000 INFO @ Tue, 10 Dec 2019 13:49:00: 8000000 INFO @ Tue, 10 Dec 2019 13:49:02: 3000000 INFO @ Tue, 10 Dec 2019 13:49:06: 6000000 INFO @ Tue, 10 Dec 2019 13:49:10: 9000000 INFO @ Tue, 10 Dec 2019 13:49:13: 4000000 INFO @ Tue, 10 Dec 2019 13:49:17: 7000000 INFO @ Tue, 10 Dec 2019 13:49:21: 10000000 INFO @ Tue, 10 Dec 2019 13:49:22: 5000000 INFO @ Tue, 10 Dec 2019 13:49:28: 8000000 INFO @ Tue, 10 Dec 2019 13:49:31: 6000000 INFO @ Tue, 10 Dec 2019 13:49:33: 11000000 INFO @ Tue, 10 Dec 2019 13:49:38: 9000000 INFO @ Tue, 10 Dec 2019 13:49:41: 7000000 INFO @ Tue, 10 Dec 2019 13:49:46: 12000000 INFO @ Tue, 10 Dec 2019 13:49:49: 10000000 INFO @ Tue, 10 Dec 2019 13:49:51: 8000000 INFO @ Tue, 10 Dec 2019 13:49:58: 13000000 INFO @ Tue, 10 Dec 2019 13:50:00: 9000000 INFO @ Tue, 10 Dec 2019 13:50:00: 11000000 INFO @ Tue, 10 Dec 2019 13:50:10: 14000000 INFO @ Tue, 10 Dec 2019 13:50:10: 10000000 INFO @ Tue, 10 Dec 2019 13:50:12: 12000000 INFO @ Tue, 10 Dec 2019 13:50:20: 11000000 INFO @ Tue, 10 Dec 2019 13:50:21: 15000000 INFO @ Tue, 10 Dec 2019 13:50:23: 13000000 INFO @ Tue, 10 Dec 2019 13:50:30: 12000000 INFO @ Tue, 10 Dec 2019 13:50:31: 16000000 INFO @ Tue, 10 Dec 2019 13:50:34: 14000000 INFO @ Tue, 10 Dec 2019 13:50:40: 13000000 INFO @ Tue, 10 Dec 2019 13:50:41: 17000000 INFO @ Tue, 10 Dec 2019 13:50:45: 15000000 INFO @ Tue, 10 Dec 2019 13:50:50: 14000000 INFO @ Tue, 10 Dec 2019 13:50:52: 18000000 INFO @ Tue, 10 Dec 2019 13:50:56: 16000000 INFO @ Tue, 10 Dec 2019 13:51:00: 15000000 INFO @ Tue, 10 Dec 2019 13:51:03: 19000000 INFO @ Tue, 10 Dec 2019 13:51:06: 17000000 INFO @ Tue, 10 Dec 2019 13:51:10: 16000000 INFO @ Tue, 10 Dec 2019 13:51:15: 20000000 INFO @ Tue, 10 Dec 2019 13:51:16: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:51:16: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:51:16: #1 total tags in treatment: 20056148 INFO @ Tue, 10 Dec 2019 13:51:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:51:16: #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 13:51:16: #1 tags after filtering in treatment: 20056003 INFO @ Tue, 10 Dec 2019 13:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:51:16: #1 finished! INFO @ Tue, 10 Dec 2019 13:51:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:51:17: 18000000 INFO @ Tue, 10 Dec 2019 13:51:19: 17000000 INFO @ Tue, 10 Dec 2019 13:51:19: #2 number of paired peaks: 5057 INFO @ Tue, 10 Dec 2019 13:51:19: start model_add_line... INFO @ Tue, 10 Dec 2019 13:51:19: start X-correlation... INFO @ Tue, 10 Dec 2019 13:51:19: end of X-cor INFO @ Tue, 10 Dec 2019 13:51:19: #2 finished! INFO @ Tue, 10 Dec 2019 13:51:19: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:51:19: #2 alternative fragment length(s) may be 84,541 bps INFO @ Tue, 10 Dec 2019 13:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.05_model.r WARNING @ Tue, 10 Dec 2019 13:51:19: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:51:19: #2 You may need to consider one of the other alternative d(s): 84,541 WARNING @ Tue, 10 Dec 2019 13:51:19: #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 13:51:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:51:28: 19000000 INFO @ Tue, 10 Dec 2019 13:51:29: 18000000 INFO @ Tue, 10 Dec 2019 13:51:38: 19000000 INFO @ Tue, 10 Dec 2019 13:51:39: 20000000 INFO @ Tue, 10 Dec 2019 13:51:40: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:51:40: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:51:40: #1 total tags in treatment: 20056148 INFO @ Tue, 10 Dec 2019 13:51:40: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:51:40: #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 13:51:41: #1 tags after filtering in treatment: 20056003 INFO @ Tue, 10 Dec 2019 13:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:51:41: #1 finished! INFO @ Tue, 10 Dec 2019 13:51:41: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:51:43: #2 number of paired peaks: 5057 INFO @ Tue, 10 Dec 2019 13:51:43: start model_add_line... INFO @ Tue, 10 Dec 2019 13:51:44: start X-correlation... INFO @ Tue, 10 Dec 2019 13:51:44: end of X-cor INFO @ Tue, 10 Dec 2019 13:51:44: #2 finished! INFO @ Tue, 10 Dec 2019 13:51:44: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:51:44: #2 alternative fragment length(s) may be 84,541 bps INFO @ Tue, 10 Dec 2019 13:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.10_model.r WARNING @ Tue, 10 Dec 2019 13:51:44: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:51:44: #2 You may need to consider one of the other alternative d(s): 84,541 WARNING @ Tue, 10 Dec 2019 13:51:44: #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 13:51:44: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:51:47: 20000000 INFO @ Tue, 10 Dec 2019 13:51:48: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:51:48: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:51:48: #1 total tags in treatment: 20056148 INFO @ Tue, 10 Dec 2019 13:51:48: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:51:48: #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 13:51:49: #1 tags after filtering in treatment: 20056003 INFO @ Tue, 10 Dec 2019 13:51:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:51:49: #1 finished! INFO @ Tue, 10 Dec 2019 13:51:49: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:51:51: #2 number of paired peaks: 5057 INFO @ Tue, 10 Dec 2019 13:51:51: start model_add_line... INFO @ Tue, 10 Dec 2019 13:51:51: start X-correlation... INFO @ Tue, 10 Dec 2019 13:51:51: end of X-cor INFO @ Tue, 10 Dec 2019 13:51:51: #2 finished! INFO @ Tue, 10 Dec 2019 13:51:51: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:51:51: #2 alternative fragment length(s) may be 84,541 bps INFO @ Tue, 10 Dec 2019 13:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.20_model.r WARNING @ Tue, 10 Dec 2019 13:51:51: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:51:51: #2 You may need to consider one of the other alternative d(s): 84,541 WARNING @ Tue, 10 Dec 2019 13:51:51: #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 13:51:51: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:52:32: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:52:56: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:52:57: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.05_summits.bed INFO @ Tue, 10 Dec 2019 13:53:12: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.20_summits.bed INFO @ Tue, 10 Dec 2019 13:53:27: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460578/SRX5460578.10_summits.bed INFO @ Tue, 10 Dec 2019 13:53:32: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。