Job ID = 4287196 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T02:49:55 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 ) 2019-12-10T02:49:55 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 ) 2019-12-10T02:50:46 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 ) 2019-12-10T02:50:46 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 : 15,252,108 reads read : 30,504,216 reads written : 15,252,108 reads 0-length : 15,252,108 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: 00:00:00 Multiseed full-index search: 00:06:47 15252108 reads; of these: 15252108 (100.00%) were unpaired; of these: 9266490 (60.76%) aligned 0 times 4023177 (26.38%) aligned exactly 1 time 1962441 (12.87%) aligned >1 times 39.24% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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_rmdupse_core] 295448 / 5985618 = 0.0494 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.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 12:03:47: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:03:47: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:03:54: 1000000 INFO @ Tue, 10 Dec 2019 12:04:00: 2000000 INFO @ Tue, 10 Dec 2019 12:04:07: 3000000 INFO @ Tue, 10 Dec 2019 12:04:13: 4000000 INFO @ Tue, 10 Dec 2019 12:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.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 12:04:17: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:04:17: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:04:20: 5000000 INFO @ Tue, 10 Dec 2019 12:04:24: 1000000 INFO @ Tue, 10 Dec 2019 12:04:25: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:04:25: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:04:25: #1 total tags in treatment: 5690170 INFO @ Tue, 10 Dec 2019 12:04:25: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:04:25: #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 12:04:25: #1 tags after filtering in treatment: 5689916 INFO @ Tue, 10 Dec 2019 12:04:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:04:25: #1 finished! INFO @ Tue, 10 Dec 2019 12:04:25: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:04:27: #2 number of paired peaks: 8012 INFO @ Tue, 10 Dec 2019 12:04:27: start model_add_line... INFO @ Tue, 10 Dec 2019 12:04:27: start X-correlation... INFO @ Tue, 10 Dec 2019 12:04:27: end of X-cor INFO @ Tue, 10 Dec 2019 12:04:27: #2 finished! INFO @ Tue, 10 Dec 2019 12:04:27: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:04:27: #2 alternative fragment length(s) may be 51,122,162,238,580 bps INFO @ Tue, 10 Dec 2019 12:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.05_model.r WARNING @ Tue, 10 Dec 2019 12:04:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:04:27: #2 You may need to consider one of the other alternative d(s): 51,122,162,238,580 WARNING @ Tue, 10 Dec 2019 12:04:27: #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 12:04:27: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:04:32: 2000000 INFO @ Tue, 10 Dec 2019 12:04:39: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:04:45: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:04:46: 4000000 INFO @ Tue, 10 Dec 2019 12:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.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 12:04:47: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:04:47: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:04:53: 5000000 INFO @ Tue, 10 Dec 2019 12:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.05_summits.bed INFO @ Tue, 10 Dec 2019 12:04:54: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:04:55: 1000000 INFO @ Tue, 10 Dec 2019 12:04:59: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:04:59: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:04:59: #1 total tags in treatment: 5690170 INFO @ Tue, 10 Dec 2019 12:04:59: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:04:59: #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 12:04:59: #1 tags after filtering in treatment: 5689916 INFO @ Tue, 10 Dec 2019 12:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:04:59: #1 finished! INFO @ Tue, 10 Dec 2019 12:04:59: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:05:01: #2 number of paired peaks: 8012 INFO @ Tue, 10 Dec 2019 12:05:01: start model_add_line... INFO @ Tue, 10 Dec 2019 12:05:01: start X-correlation... INFO @ Tue, 10 Dec 2019 12:05:01: end of X-cor INFO @ Tue, 10 Dec 2019 12:05:01: #2 finished! INFO @ Tue, 10 Dec 2019 12:05:01: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:05:01: #2 alternative fragment length(s) may be 51,122,162,238,580 bps INFO @ Tue, 10 Dec 2019 12:05:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.10_model.r WARNING @ Tue, 10 Dec 2019 12:05:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:05:01: #2 You may need to consider one of the other alternative d(s): 51,122,162,238,580 WARNING @ Tue, 10 Dec 2019 12:05:01: #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 12:05:01: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:05:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:05:02: 2000000 INFO @ Tue, 10 Dec 2019 12:05:09: 3000000 INFO @ Tue, 10 Dec 2019 12:05:17: 4000000 INFO @ Tue, 10 Dec 2019 12:05:19: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:05:24: 5000000 INFO @ Tue, 10 Dec 2019 12:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.10_summits.bed INFO @ Tue, 10 Dec 2019 12:05:28: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (416 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:05:29: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:05:29: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:05:29: #1 total tags in treatment: 5690170 INFO @ Tue, 10 Dec 2019 12:05:29: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:05:29: #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 12:05:29: #1 tags after filtering in treatment: 5689916 INFO @ Tue, 10 Dec 2019 12:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:05:29: #1 finished! INFO @ Tue, 10 Dec 2019 12:05:29: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:05:31: #2 number of paired peaks: 8012 INFO @ Tue, 10 Dec 2019 12:05:31: start model_add_line... INFO @ Tue, 10 Dec 2019 12:05:31: start X-correlation... INFO @ Tue, 10 Dec 2019 12:05:31: end of X-cor INFO @ Tue, 10 Dec 2019 12:05:31: #2 finished! INFO @ Tue, 10 Dec 2019 12:05:31: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:05:31: #2 alternative fragment length(s) may be 51,122,162,238,580 bps INFO @ Tue, 10 Dec 2019 12:05:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.20_model.r WARNING @ Tue, 10 Dec 2019 12:05:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:05:31: #2 You may need to consider one of the other alternative d(s): 51,122,162,238,580 WARNING @ Tue, 10 Dec 2019 12:05:31: #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 12:05:31: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:05:49: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654055/SRX4654055.20_summits.bed INFO @ Tue, 10 Dec 2019 12:05:58: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (172 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。