Job ID = 4288927 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:35:08 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 ) 2019-12-10T03:39:06 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 ) 2019-12-10T03:39:06 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 : 12,612,944 reads read : 25,225,888 reads written : 12,612,944 reads 0-length : 12,612,944 2019-12-10T03:46:20 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 12,761,297 reads read : 25,522,594 reads written : 12,761,297 reads 0-length : 12,761,297 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:29:35 25374241 reads; of these: 25374241 (100.00%) were unpaired; of these: 1087402 (4.29%) aligned 0 times 18139532 (71.49%) aligned exactly 1 time 6147307 (24.23%) aligned >1 times 95.71% overall alignment rate Time searching: 00:29:36 Overall time: 00:29:36 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] 1965412 / 24286839 = 0.0809 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.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 13:32:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:32:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:33:08: 1000000 INFO @ Tue, 10 Dec 2019 13:33:16: 2000000 INFO @ Tue, 10 Dec 2019 13:33:25: 3000000 INFO @ Tue, 10 Dec 2019 13:33:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.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 13:33:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:33:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:33:34: 4000000 INFO @ Tue, 10 Dec 2019 13:33:39: 1000000 INFO @ Tue, 10 Dec 2019 13:33:43: 5000000 INFO @ Tue, 10 Dec 2019 13:33:50: 2000000 INFO @ Tue, 10 Dec 2019 13:33:52: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:33:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.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 13:33:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:33:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:34:00: 3000000 INFO @ Tue, 10 Dec 2019 13:34:01: 7000000 INFO @ Tue, 10 Dec 2019 13:34:10: 8000000 INFO @ Tue, 10 Dec 2019 13:34:10: 1000000 INFO @ Tue, 10 Dec 2019 13:34:11: 4000000 INFO @ Tue, 10 Dec 2019 13:34:19: 9000000 INFO @ Tue, 10 Dec 2019 13:34:20: 2000000 INFO @ Tue, 10 Dec 2019 13:34:21: 5000000 INFO @ Tue, 10 Dec 2019 13:34:28: 10000000 INFO @ Tue, 10 Dec 2019 13:34:31: 3000000 INFO @ Tue, 10 Dec 2019 13:34:32: 6000000 INFO @ Tue, 10 Dec 2019 13:34:37: 11000000 INFO @ Tue, 10 Dec 2019 13:34:42: 4000000 INFO @ Tue, 10 Dec 2019 13:34:42: 7000000 INFO @ Tue, 10 Dec 2019 13:34:46: 12000000 INFO @ Tue, 10 Dec 2019 13:34:52: 5000000 INFO @ Tue, 10 Dec 2019 13:34:53: 8000000 INFO @ Tue, 10 Dec 2019 13:34:54: 13000000 INFO @ Tue, 10 Dec 2019 13:35:03: 6000000 INFO @ Tue, 10 Dec 2019 13:35:03: 9000000 INFO @ Tue, 10 Dec 2019 13:35:03: 14000000 INFO @ Tue, 10 Dec 2019 13:35:12: 15000000 INFO @ Tue, 10 Dec 2019 13:35:14: 7000000 INFO @ Tue, 10 Dec 2019 13:35:14: 10000000 INFO @ Tue, 10 Dec 2019 13:35:21: 16000000 INFO @ Tue, 10 Dec 2019 13:35:24: 11000000 INFO @ Tue, 10 Dec 2019 13:35:25: 8000000 INFO @ Tue, 10 Dec 2019 13:35:30: 17000000 INFO @ Tue, 10 Dec 2019 13:35:35: 12000000 INFO @ Tue, 10 Dec 2019 13:35:35: 9000000 INFO @ Tue, 10 Dec 2019 13:35:39: 18000000 INFO @ Tue, 10 Dec 2019 13:35:45: 13000000 INFO @ Tue, 10 Dec 2019 13:35:46: 10000000 INFO @ Tue, 10 Dec 2019 13:35:48: 19000000 INFO @ Tue, 10 Dec 2019 13:35:55: 14000000 INFO @ Tue, 10 Dec 2019 13:35:56: 11000000 INFO @ Tue, 10 Dec 2019 13:35:57: 20000000 INFO @ Tue, 10 Dec 2019 13:36:06: 15000000 INFO @ Tue, 10 Dec 2019 13:36:06: 21000000 INFO @ Tue, 10 Dec 2019 13:36:07: 12000000 INFO @ Tue, 10 Dec 2019 13:36:15: 22000000 INFO @ Tue, 10 Dec 2019 13:36:16: 16000000 INFO @ Tue, 10 Dec 2019 13:36:17: 13000000 INFO @ Tue, 10 Dec 2019 13:36:19: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:36:19: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:36:19: #1 total tags in treatment: 22321427 INFO @ Tue, 10 Dec 2019 13:36:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:36:19: #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 13:36:19: #1 tags after filtering in treatment: 22321294 INFO @ Tue, 10 Dec 2019 13:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:36:19: #1 finished! INFO @ Tue, 10 Dec 2019 13:36:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:36:22: #2 number of paired peaks: 4913 INFO @ Tue, 10 Dec 2019 13:36:22: start model_add_line... INFO @ Tue, 10 Dec 2019 13:36:22: start X-correlation... INFO @ Tue, 10 Dec 2019 13:36:22: end of X-cor INFO @ Tue, 10 Dec 2019 13:36:22: #2 finished! INFO @ Tue, 10 Dec 2019 13:36:22: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:36:22: #2 alternative fragment length(s) may be 84,518 bps INFO @ Tue, 10 Dec 2019 13:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.05_model.r WARNING @ Tue, 10 Dec 2019 13:36:22: #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 13:36:22: #2 You may need to consider one of the other alternative d(s): 84,518 WARNING @ Tue, 10 Dec 2019 13:36:22: #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 13:36:22: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:36:27: 17000000 INFO @ Tue, 10 Dec 2019 13:36:28: 14000000 INFO @ Tue, 10 Dec 2019 13:36:37: 18000000 INFO @ Tue, 10 Dec 2019 13:36:38: 15000000 INFO @ Tue, 10 Dec 2019 13:36:47: 19000000 INFO @ Tue, 10 Dec 2019 13:36:48: 16000000 INFO @ Tue, 10 Dec 2019 13:36:57: 20000000 INFO @ Tue, 10 Dec 2019 13:36:59: 17000000 INFO @ Tue, 10 Dec 2019 13:37:08: 21000000 INFO @ Tue, 10 Dec 2019 13:37:09: 18000000 INFO @ Tue, 10 Dec 2019 13:37:18: 22000000 INFO @ Tue, 10 Dec 2019 13:37:19: 19000000 INFO @ Tue, 10 Dec 2019 13:37:22: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:37:22: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:37:22: #1 total tags in treatment: 22321427 INFO @ Tue, 10 Dec 2019 13:37:22: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:37:22: #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 13:37:22: #1 tags after filtering in treatment: 22321294 INFO @ Tue, 10 Dec 2019 13:37:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:37:22: #1 finished! INFO @ Tue, 10 Dec 2019 13:37:22: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:37:25: #2 number of paired peaks: 4913 INFO @ Tue, 10 Dec 2019 13:37:25: start model_add_line... INFO @ Tue, 10 Dec 2019 13:37:25: start X-correlation... INFO @ Tue, 10 Dec 2019 13:37:25: end of X-cor INFO @ Tue, 10 Dec 2019 13:37:25: #2 finished! INFO @ Tue, 10 Dec 2019 13:37:25: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:37:25: #2 alternative fragment length(s) may be 84,518 bps INFO @ Tue, 10 Dec 2019 13:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.10_model.r WARNING @ Tue, 10 Dec 2019 13:37:25: #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 13:37:25: #2 You may need to consider one of the other alternative d(s): 84,518 WARNING @ Tue, 10 Dec 2019 13:37:25: #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 13:37:25: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:37:30: 20000000 INFO @ Tue, 10 Dec 2019 13:37:32: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:37:40: 21000000 INFO @ Tue, 10 Dec 2019 13:37:50: 22000000 INFO @ Tue, 10 Dec 2019 13:37:54: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:37:54: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:37:54: #1 total tags in treatment: 22321427 INFO @ Tue, 10 Dec 2019 13:37:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:37:54: #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 13:37:54: #1 tags after filtering in treatment: 22321294 INFO @ Tue, 10 Dec 2019 13:37:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:37:54: #1 finished! INFO @ Tue, 10 Dec 2019 13:37:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:37:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:37:57: #2 number of paired peaks: 4913 INFO @ Tue, 10 Dec 2019 13:37:57: start model_add_line... INFO @ Tue, 10 Dec 2019 13:37:57: start X-correlation... INFO @ Tue, 10 Dec 2019 13:37:57: end of X-cor INFO @ Tue, 10 Dec 2019 13:37:57: #2 finished! INFO @ Tue, 10 Dec 2019 13:37:57: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:37:57: #2 alternative fragment length(s) may be 84,518 bps INFO @ Tue, 10 Dec 2019 13:37:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.20_model.r WARNING @ Tue, 10 Dec 2019 13:37:57: #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 13:37:57: #2 You may need to consider one of the other alternative d(s): 84,518 WARNING @ Tue, 10 Dec 2019 13:37:57: #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 13:37:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:37:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.05_summits.bed INFO @ Tue, 10 Dec 2019 13:38:09: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1212 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:38:36: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:39:08: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.10_summits.bed INFO @ Tue, 10 Dec 2019 13:39:12: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460566/SRX5460566.20_summits.bed INFO @ Tue, 10 Dec 2019 13:39:44: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (384 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。