Job ID = 1294235 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:49:04 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 ) 2019-06-02T20:49:04 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 ) 2019-06-02T20:49:04 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 : 173,984,085 reads read : 173,984,085 reads written : 173,984,085 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:38:34 173984085 reads; of these: 173984085 (100.00%) were unpaired; of these: 85062401 (48.89%) aligned 0 times 70351225 (40.44%) aligned exactly 1 time 18570459 (10.67%) aligned >1 times 51.11% overall alignment rate Time searching: 00:38:34 Overall time: 00:38:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 40 files... [bam_rmdupse_core] 76318252 / 88921684 = 0.8583 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 06:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 06:47:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:47:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 06:47:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:47:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 06:47:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:47:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:48:03: 1000000 INFO @ Mon, 03 Jun 2019 06:48:03: 1000000 INFO @ Mon, 03 Jun 2019 06:48:04: 1000000 INFO @ Mon, 03 Jun 2019 06:48:09: 2000000 INFO @ Mon, 03 Jun 2019 06:48:10: 2000000 INFO @ Mon, 03 Jun 2019 06:48:12: 2000000 INFO @ Mon, 03 Jun 2019 06:48:16: 3000000 INFO @ Mon, 03 Jun 2019 06:48:18: 3000000 INFO @ Mon, 03 Jun 2019 06:48:21: 3000000 INFO @ Mon, 03 Jun 2019 06:48:23: 4000000 INFO @ Mon, 03 Jun 2019 06:48:25: 4000000 INFO @ Mon, 03 Jun 2019 06:48:29: 4000000 INFO @ Mon, 03 Jun 2019 06:48:29: 5000000 INFO @ Mon, 03 Jun 2019 06:48:32: 5000000 INFO @ Mon, 03 Jun 2019 06:48:36: 6000000 INFO @ Mon, 03 Jun 2019 06:48:37: 5000000 INFO @ Mon, 03 Jun 2019 06:48:39: 6000000 INFO @ Mon, 03 Jun 2019 06:48:42: 7000000 INFO @ Mon, 03 Jun 2019 06:48:45: 6000000 INFO @ Mon, 03 Jun 2019 06:48:46: 7000000 INFO @ Mon, 03 Jun 2019 06:48:49: 8000000 INFO @ Mon, 03 Jun 2019 06:48:53: 7000000 INFO @ Mon, 03 Jun 2019 06:48:53: 8000000 INFO @ Mon, 03 Jun 2019 06:48:55: 9000000 INFO @ Mon, 03 Jun 2019 06:49:00: 9000000 INFO @ Mon, 03 Jun 2019 06:49:01: 8000000 INFO @ Mon, 03 Jun 2019 06:49:02: 10000000 INFO @ Mon, 03 Jun 2019 06:49:07: 10000000 INFO @ Mon, 03 Jun 2019 06:49:08: 11000000 INFO @ Mon, 03 Jun 2019 06:49:09: 9000000 INFO @ Mon, 03 Jun 2019 06:49:14: 11000000 INFO @ Mon, 03 Jun 2019 06:49:15: 12000000 INFO @ Mon, 03 Jun 2019 06:49:17: 10000000 INFO @ Mon, 03 Jun 2019 06:49:19: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:49:19: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:49:19: #1 total tags in treatment: 12603432 INFO @ Mon, 03 Jun 2019 06:49:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:49:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:49:19: #1 tags after filtering in treatment: 12603432 INFO @ Mon, 03 Jun 2019 06:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:49:19: #1 finished! INFO @ Mon, 03 Jun 2019 06:49:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:49:21: #2 number of paired peaks: 2242 INFO @ Mon, 03 Jun 2019 06:49:21: start model_add_line... INFO @ Mon, 03 Jun 2019 06:49:21: start X-correlation... INFO @ Mon, 03 Jun 2019 06:49:21: end of X-cor INFO @ Mon, 03 Jun 2019 06:49:21: #2 finished! INFO @ Mon, 03 Jun 2019 06:49:21: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 06:49:21: #2 alternative fragment length(s) may be 4,58 bps INFO @ Mon, 03 Jun 2019 06:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.10_model.r WARNING @ Mon, 03 Jun 2019 06:49:21: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:49:21: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Mon, 03 Jun 2019 06:49:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:49:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:49:21: 12000000 INFO @ Mon, 03 Jun 2019 06:49:25: 11000000 INFO @ Mon, 03 Jun 2019 06:49:26: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:49:26: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:49:26: #1 total tags in treatment: 12603432 INFO @ Mon, 03 Jun 2019 06:49:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:49:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:49:26: #1 tags after filtering in treatment: 12603432 INFO @ Mon, 03 Jun 2019 06:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:49:26: #1 finished! INFO @ Mon, 03 Jun 2019 06:49:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:49:27: #2 number of paired peaks: 2242 INFO @ Mon, 03 Jun 2019 06:49:27: start model_add_line... INFO @ Mon, 03 Jun 2019 06:49:27: start X-correlation... INFO @ Mon, 03 Jun 2019 06:49:27: end of X-cor INFO @ Mon, 03 Jun 2019 06:49:27: #2 finished! INFO @ Mon, 03 Jun 2019 06:49:27: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 06:49:27: #2 alternative fragment length(s) may be 4,58 bps INFO @ Mon, 03 Jun 2019 06:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.05_model.r WARNING @ Mon, 03 Jun 2019 06:49:27: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:49:27: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Mon, 03 Jun 2019 06:49:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:49:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:49:32: 12000000 INFO @ Mon, 03 Jun 2019 06:49:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:49:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:49:38: #1 total tags in treatment: 12603432 INFO @ Mon, 03 Jun 2019 06:49:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:49:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:49:38: #1 tags after filtering in treatment: 12603432 INFO @ Mon, 03 Jun 2019 06:49:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:49:38: #1 finished! INFO @ Mon, 03 Jun 2019 06:49:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:49:39: #2 number of paired peaks: 2242 INFO @ Mon, 03 Jun 2019 06:49:39: start model_add_line... INFO @ Mon, 03 Jun 2019 06:49:39: start X-correlation... INFO @ Mon, 03 Jun 2019 06:49:39: end of X-cor INFO @ Mon, 03 Jun 2019 06:49:39: #2 finished! INFO @ Mon, 03 Jun 2019 06:49:39: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 06:49:39: #2 alternative fragment length(s) may be 4,58 bps INFO @ Mon, 03 Jun 2019 06:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.20_model.r WARNING @ Mon, 03 Jun 2019 06:49:39: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:49:39: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Mon, 03 Jun 2019 06:49:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:49:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:49:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:49:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:50:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.10_summits.bed INFO @ Mon, 03 Jun 2019 06:50:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6024 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:50:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.05_summits.bed INFO @ Mon, 03 Jun 2019 06:50:21: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (16115 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202124/SRX202124.20_summits.bed INFO @ Mon, 03 Jun 2019 06:50:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2411 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。