Job ID = 5721030 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:35:42 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 : 9,407,890 reads read : 9,407,890 reads written : 9,407,890 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:09 9407890 reads; of these: 9407890 (100.00%) were unpaired; of these: 1170389 (12.44%) aligned 0 times 5911250 (62.83%) aligned exactly 1 time 2326251 (24.73%) aligned >1 times 87.56% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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_rmdupse_core] 1322226 / 8237501 = 0.1605 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 03:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.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 03:44:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:44:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:44:45: 1000000 INFO @ Thu, 16 Apr 2020 03:44:51: 2000000 INFO @ Thu, 16 Apr 2020 03:44:56: 3000000 INFO @ Thu, 16 Apr 2020 03:45:01: 4000000 INFO @ Thu, 16 Apr 2020 03:45:06: 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 03:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.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 03:45:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:45:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:45:11: 6000000 INFO @ Thu, 16 Apr 2020 03:45:16: 1000000 INFO @ Thu, 16 Apr 2020 03:45:16: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:45:16: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:45:16: #1 total tags in treatment: 6915275 INFO @ Thu, 16 Apr 2020 03:45:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:16: #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 03:45:16: #1 tags after filtering in treatment: 6915275 INFO @ Thu, 16 Apr 2020 03:45:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:16: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:17: #2 number of paired peaks: 221 WARNING @ Thu, 16 Apr 2020 03:45:17: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:17: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:17: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:17: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:17: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:17: #2 predicted fragment length is 156 bps INFO @ Thu, 16 Apr 2020 03:45:17: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 16 Apr 2020 03:45:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.05_model.r INFO @ Thu, 16 Apr 2020 03:45:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:21: 2000000 INFO @ Thu, 16 Apr 2020 03:45:26: 3000000 INFO @ Thu, 16 Apr 2020 03:45:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:45:31: 4000000 INFO @ Thu, 16 Apr 2020 03:45:37: 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 03:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.05_summits.bed INFO @ Thu, 16 Apr 2020 03:45:39: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1675 records, 4 fields): 3 millis INFO @ Thu, 16 Apr 2020 03:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.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 03:45:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:45:40: #1 read treatment tags... CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:45:42: 6000000 INFO @ Thu, 16 Apr 2020 03:45:46: 1000000 INFO @ Thu, 16 Apr 2020 03:45:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:45:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:45:47: #1 total tags in treatment: 6915275 INFO @ Thu, 16 Apr 2020 03:45:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:47: #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 03:45:47: #1 tags after filtering in treatment: 6915275 INFO @ Thu, 16 Apr 2020 03:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:47: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:48: #2 number of paired peaks: 221 WARNING @ Thu, 16 Apr 2020 03:45:48: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:48: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:48: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:48: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:48: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:48: #2 predicted fragment length is 156 bps INFO @ Thu, 16 Apr 2020 03:45:48: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 16 Apr 2020 03:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.10_model.r INFO @ Thu, 16 Apr 2020 03:45:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:51: 2000000 INFO @ Thu, 16 Apr 2020 03:45:57: 3000000 INFO @ Thu, 16 Apr 2020 03:46:02: 4000000 INFO @ Thu, 16 Apr 2020 03:46:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:46:08: 5000000 INFO @ Thu, 16 Apr 2020 03:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.10_summits.bed INFO @ Thu, 16 Apr 2020 03:46:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:46:13: 6000000 INFO @ Thu, 16 Apr 2020 03:46:18: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:46:18: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:46:18: #1 total tags in treatment: 6915275 INFO @ Thu, 16 Apr 2020 03:46:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:46:18: #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 03:46:18: #1 tags after filtering in treatment: 6915275 INFO @ Thu, 16 Apr 2020 03:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:46:18: #1 finished! INFO @ Thu, 16 Apr 2020 03:46:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:46:19: #2 number of paired peaks: 221 WARNING @ Thu, 16 Apr 2020 03:46:19: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Thu, 16 Apr 2020 03:46:19: start model_add_line... INFO @ Thu, 16 Apr 2020 03:46:19: start X-correlation... INFO @ Thu, 16 Apr 2020 03:46:19: end of X-cor INFO @ Thu, 16 Apr 2020 03:46:19: #2 finished! INFO @ Thu, 16 Apr 2020 03:46:19: #2 predicted fragment length is 156 bps INFO @ Thu, 16 Apr 2020 03:46:19: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 16 Apr 2020 03:46:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.20_model.r INFO @ Thu, 16 Apr 2020 03:46:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:46:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386769/SRX6386769.20_summits.bed INFO @ Thu, 16 Apr 2020 03:46:40: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (405 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。