Job ID = 5720734 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:05:24 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 : 15,845,425 reads read : 31,690,850 reads written : 15,845,425 reads 0-length : 15,845,425 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:09 15845425 reads; of these: 15845425 (100.00%) were unpaired; of these: 1581553 (9.98%) aligned 0 times 10353585 (65.34%) aligned exactly 1 time 3910287 (24.68%) aligned >1 times 90.02% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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 8 files... [bam_rmdupse_core] 1449313 / 14263872 = 0.1016 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 01:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.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 @ Thu, 16 Apr 2020 01:21:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:21:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:21:48: 1000000 INFO @ Thu, 16 Apr 2020 01:21:53: 2000000 INFO @ Thu, 16 Apr 2020 01:21:58: 3000000 INFO @ Thu, 16 Apr 2020 01:22:03: 4000000 INFO @ Thu, 16 Apr 2020 01:22:08: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 01:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.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 @ Thu, 16 Apr 2020 01:22:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:22:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:22:13: 6000000 INFO @ Thu, 16 Apr 2020 01:22:16: 1000000 INFO @ Thu, 16 Apr 2020 01:22:18: 7000000 INFO @ Thu, 16 Apr 2020 01:22:22: 2000000 INFO @ Thu, 16 Apr 2020 01:22:23: 8000000 INFO @ Thu, 16 Apr 2020 01:22:27: 3000000 INFO @ Thu, 16 Apr 2020 01:22:28: 9000000 INFO @ Thu, 16 Apr 2020 01:22:32: 4000000 INFO @ Thu, 16 Apr 2020 01:22:33: 10000000 INFO @ Thu, 16 Apr 2020 01:22:37: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 01:22:39: 11000000 INFO @ Thu, 16 Apr 2020 01:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.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 @ Thu, 16 Apr 2020 01:22:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:22:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:22:42: 6000000 INFO @ Thu, 16 Apr 2020 01:22:44: 12000000 INFO @ Thu, 16 Apr 2020 01:22:47: 1000000 INFO @ Thu, 16 Apr 2020 01:22:48: 7000000 INFO @ Thu, 16 Apr 2020 01:22:48: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:22:48: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:22:48: #1 total tags in treatment: 12814559 INFO @ Thu, 16 Apr 2020 01:22:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:22:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:22:48: #1 tags after filtering in treatment: 12814559 INFO @ Thu, 16 Apr 2020 01:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:22:48: #1 finished! INFO @ Thu, 16 Apr 2020 01:22:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:22:49: #2 number of paired peaks: 674 WARNING @ Thu, 16 Apr 2020 01:22:49: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Thu, 16 Apr 2020 01:22:49: start model_add_line... INFO @ Thu, 16 Apr 2020 01:22:49: start X-correlation... INFO @ Thu, 16 Apr 2020 01:22:49: end of X-cor INFO @ Thu, 16 Apr 2020 01:22:49: #2 finished! INFO @ Thu, 16 Apr 2020 01:22:49: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:22:49: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.05_model.r WARNING @ Thu, 16 Apr 2020 01:22:49: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:22:49: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:22:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:22:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:22:52: 2000000 INFO @ Thu, 16 Apr 2020 01:22:53: 8000000 INFO @ Thu, 16 Apr 2020 01:22:57: 3000000 INFO @ Thu, 16 Apr 2020 01:22:58: 9000000 INFO @ Thu, 16 Apr 2020 01:23:02: 4000000 INFO @ Thu, 16 Apr 2020 01:23:03: 10000000 INFO @ Thu, 16 Apr 2020 01:23:07: 5000000 INFO @ Thu, 16 Apr 2020 01:23:08: 11000000 INFO @ Thu, 16 Apr 2020 01:23:12: 6000000 INFO @ Thu, 16 Apr 2020 01:23:13: 12000000 INFO @ Thu, 16 Apr 2020 01:23:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:23:17: 7000000 INFO @ Thu, 16 Apr 2020 01:23:18: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:23:18: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:23:18: #1 total tags in treatment: 12814559 INFO @ Thu, 16 Apr 2020 01:23:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:23:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:23:18: #1 tags after filtering in treatment: 12814559 INFO @ Thu, 16 Apr 2020 01:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:23:18: #1 finished! INFO @ Thu, 16 Apr 2020 01:23:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:23:19: #2 number of paired peaks: 674 WARNING @ Thu, 16 Apr 2020 01:23:19: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Thu, 16 Apr 2020 01:23:19: start model_add_line... INFO @ Thu, 16 Apr 2020 01:23:19: start X-correlation... INFO @ Thu, 16 Apr 2020 01:23:19: end of X-cor INFO @ Thu, 16 Apr 2020 01:23:19: #2 finished! INFO @ Thu, 16 Apr 2020 01:23:19: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:23:19: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.10_model.r WARNING @ Thu, 16 Apr 2020 01:23:19: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:23:19: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:23:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:23:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:23:23: 8000000 INFO @ Thu, 16 Apr 2020 01:23:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:23:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.05_summits.bed INFO @ Thu, 16 Apr 2020 01:23:27: Done! INFO @ Thu, 16 Apr 2020 01:23:28: 9000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4268 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:23:33: 10000000 INFO @ Thu, 16 Apr 2020 01:23:38: 11000000 INFO @ Thu, 16 Apr 2020 01:23:43: 12000000 INFO @ Thu, 16 Apr 2020 01:23:44: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:23:47: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:23:47: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:23:47: #1 total tags in treatment: 12814559 INFO @ Thu, 16 Apr 2020 01:23:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:23:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:23:47: #1 tags after filtering in treatment: 12814559 INFO @ Thu, 16 Apr 2020 01:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:23:47: #1 finished! INFO @ Thu, 16 Apr 2020 01:23:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:23:48: #2 number of paired peaks: 674 WARNING @ Thu, 16 Apr 2020 01:23:48: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Thu, 16 Apr 2020 01:23:48: start model_add_line... INFO @ Thu, 16 Apr 2020 01:23:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:23:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:23:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:23:48: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:23:48: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.20_model.r WARNING @ Thu, 16 Apr 2020 01:23:48: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:23:48: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:23:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:23:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.10_summits.bed INFO @ Thu, 16 Apr 2020 01:23:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2163 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:24:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226973/SRX5226973.20_summits.bed INFO @ Thu, 16 Apr 2020 01:24:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (883 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。