Job ID = 4288832 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:18:07 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 ) 2019-12-10T03:18:07 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 ) 2019-12-10T03:18:07 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 : 18,314,890 reads read : 36,629,780 reads written : 18,314,890 reads 0-length : 18,314,890 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: 00:12:01 18314890 reads; of these: 18314890 (100.00%) were unpaired; of these: 9031492 (49.31%) aligned 0 times 6295978 (34.38%) aligned exactly 1 time 2987420 (16.31%) aligned >1 times 50.69% overall alignment rate Time searching: 00:12:07 Overall time: 00:12:07 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] 482608 / 9283398 = 0.0520 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:36:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.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 12:36:44: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:36:44: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:36:54: 1000000 INFO @ Tue, 10 Dec 2019 12:37:04: 2000000 INFO @ Tue, 10 Dec 2019 12:37:13: 3000000 INFO @ Tue, 10 Dec 2019 12:37:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.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 12:37:14: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:37:14: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:37:23: 4000000 INFO @ Tue, 10 Dec 2019 12:37:25: 1000000 INFO @ Tue, 10 Dec 2019 12:37:33: 5000000 INFO @ Tue, 10 Dec 2019 12:37:35: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:37:43: 6000000 INFO @ Tue, 10 Dec 2019 12:37:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.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 12:37:44: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:37:44: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:37:46: 3000000 INFO @ Tue, 10 Dec 2019 12:37:53: 1000000 INFO @ Tue, 10 Dec 2019 12:37:53: 7000000 INFO @ Tue, 10 Dec 2019 12:37:57: 4000000 INFO @ Tue, 10 Dec 2019 12:38:03: 2000000 INFO @ Tue, 10 Dec 2019 12:38:03: 8000000 INFO @ Tue, 10 Dec 2019 12:38:08: 5000000 INFO @ Tue, 10 Dec 2019 12:38:11: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:38:11: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:38:11: #1 total tags in treatment: 8800790 INFO @ Tue, 10 Dec 2019 12:38:11: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:38:11: #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 12:38:12: #1 tags after filtering in treatment: 8800563 INFO @ Tue, 10 Dec 2019 12:38:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:38:12: #1 finished! INFO @ Tue, 10 Dec 2019 12:38:12: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:38:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:38:12: 3000000 INFO @ Tue, 10 Dec 2019 12:38:13: #2 number of paired peaks: 7377 INFO @ Tue, 10 Dec 2019 12:38:13: start model_add_line... INFO @ Tue, 10 Dec 2019 12:38:13: start X-correlation... INFO @ Tue, 10 Dec 2019 12:38:13: end of X-cor INFO @ Tue, 10 Dec 2019 12:38:13: #2 finished! INFO @ Tue, 10 Dec 2019 12:38:13: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:38:13: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 10 Dec 2019 12:38:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.05_model.r WARNING @ Tue, 10 Dec 2019 12:38:13: #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 12:38:13: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 10 Dec 2019 12:38:13: #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 12:38:13: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:38:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:38:19: 6000000 INFO @ Tue, 10 Dec 2019 12:38:21: 4000000 INFO @ Tue, 10 Dec 2019 12:38:29: 7000000 INFO @ Tue, 10 Dec 2019 12:38:31: 5000000 INFO @ Tue, 10 Dec 2019 12:38:40: 6000000 INFO @ Tue, 10 Dec 2019 12:38:40: 8000000 INFO @ Tue, 10 Dec 2019 12:38:41: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:38:49: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:38:49: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:38:49: #1 total tags in treatment: 8800790 INFO @ Tue, 10 Dec 2019 12:38:49: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:38:49: #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 12:38:49: #1 tags after filtering in treatment: 8800563 INFO @ Tue, 10 Dec 2019 12:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:38:49: #1 finished! INFO @ Tue, 10 Dec 2019 12:38:49: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:38:49: 7000000 INFO @ Tue, 10 Dec 2019 12:38:51: #2 number of paired peaks: 7377 INFO @ Tue, 10 Dec 2019 12:38:51: start model_add_line... INFO @ Tue, 10 Dec 2019 12:38:51: start X-correlation... INFO @ Tue, 10 Dec 2019 12:38:51: end of X-cor INFO @ Tue, 10 Dec 2019 12:38:51: #2 finished! INFO @ Tue, 10 Dec 2019 12:38:51: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:38:51: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 10 Dec 2019 12:38:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.10_model.r WARNING @ Tue, 10 Dec 2019 12:38:51: #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 12:38:51: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 10 Dec 2019 12:38:51: #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 12:38:51: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:38:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:38:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:38:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.05_summits.bed INFO @ Tue, 10 Dec 2019 12:38:55: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (992 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:38:58: 8000000 INFO @ Tue, 10 Dec 2019 12:39:05: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:39:05: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:39:05: #1 total tags in treatment: 8800790 INFO @ Tue, 10 Dec 2019 12:39:05: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:39:05: #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 12:39:05: #1 tags after filtering in treatment: 8800563 INFO @ Tue, 10 Dec 2019 12:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:39:05: #1 finished! INFO @ Tue, 10 Dec 2019 12:39:05: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:39:07: #2 number of paired peaks: 7377 INFO @ Tue, 10 Dec 2019 12:39:07: start model_add_line... INFO @ Tue, 10 Dec 2019 12:39:07: start X-correlation... INFO @ Tue, 10 Dec 2019 12:39:07: end of X-cor INFO @ Tue, 10 Dec 2019 12:39:07: #2 finished! INFO @ Tue, 10 Dec 2019 12:39:07: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:39:07: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 10 Dec 2019 12:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.20_model.r WARNING @ Tue, 10 Dec 2019 12:39:07: #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 12:39:07: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 10 Dec 2019 12:39:07: #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 12:39:07: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:39:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:39:18: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.10_summits.bed INFO @ Tue, 10 Dec 2019 12:39:32: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:39:35: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654074/SRX4654074.20_summits.bed INFO @ Tue, 10 Dec 2019 12:39:49: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。