Job ID = 5721148 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:16:42 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 ) 2020-04-15T20:16:42 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 : 12,292,565 reads read : 24,585,130 reads written : 24,585,130 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: 00:23:50 12292565 reads; of these: 12292565 (100.00%) were paired; of these: 3248179 (26.42%) aligned concordantly 0 times 6238869 (50.75%) aligned concordantly exactly 1 time 2805517 (22.82%) aligned concordantly >1 times ---- 3248179 pairs aligned concordantly 0 times; of these: 78318 (2.41%) aligned discordantly 1 time ---- 3169861 pairs aligned 0 times concordantly or discordantly; of these: 6339722 mates make up the pairs; of these: 5953502 (93.91%) aligned 0 times 221477 (3.49%) aligned exactly 1 time 164743 (2.60%) aligned >1 times 75.78% overall alignment rate Time searching: 00:23:50 Overall time: 00:23:50 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 499330 / 9100070 = 0.0549 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 05:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.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 05:54:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:54:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:55:01: 1000000 INFO @ Thu, 16 Apr 2020 05:55:07: 2000000 INFO @ Thu, 16 Apr 2020 05:55:13: 3000000 INFO @ Thu, 16 Apr 2020 05:55:19: 4000000 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 05:55:25: 5000000 INFO @ Thu, 16 Apr 2020 05:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.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 05:55:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:55:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:55:32: 6000000 INFO @ Thu, 16 Apr 2020 05:55:33: 1000000 INFO @ Thu, 16 Apr 2020 05:55:39: 7000000 INFO @ Thu, 16 Apr 2020 05:55:42: 2000000 INFO @ Thu, 16 Apr 2020 05:55:47: 8000000 INFO @ Thu, 16 Apr 2020 05:55:50: 3000000 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 05:55:54: 9000000 INFO @ Thu, 16 Apr 2020 05:55:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.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 05:55:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:55:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:55:58: 4000000 INFO @ Thu, 16 Apr 2020 05:56:02: 10000000 INFO @ Thu, 16 Apr 2020 05:56:04: 1000000 INFO @ Thu, 16 Apr 2020 05:56:06: 5000000 INFO @ Thu, 16 Apr 2020 05:56:10: 11000000 INFO @ Thu, 16 Apr 2020 05:56:12: 2000000 INFO @ Thu, 16 Apr 2020 05:56:14: 6000000 INFO @ Thu, 16 Apr 2020 05:56:17: 12000000 INFO @ Thu, 16 Apr 2020 05:56:20: 3000000 INFO @ Thu, 16 Apr 2020 05:56:22: 7000000 INFO @ Thu, 16 Apr 2020 05:56:25: 13000000 INFO @ Thu, 16 Apr 2020 05:56:28: 4000000 INFO @ Thu, 16 Apr 2020 05:56:30: 8000000 INFO @ Thu, 16 Apr 2020 05:56:33: 14000000 INFO @ Thu, 16 Apr 2020 05:56:37: 5000000 INFO @ Thu, 16 Apr 2020 05:56:38: 9000000 INFO @ Thu, 16 Apr 2020 05:56:40: 15000000 INFO @ Thu, 16 Apr 2020 05:56:45: 6000000 INFO @ Thu, 16 Apr 2020 05:56:45: 10000000 INFO @ Thu, 16 Apr 2020 05:56:48: 16000000 INFO @ Thu, 16 Apr 2020 05:56:53: 7000000 INFO @ Thu, 16 Apr 2020 05:56:53: 11000000 INFO @ Thu, 16 Apr 2020 05:56:56: 17000000 INFO @ Thu, 16 Apr 2020 05:57:01: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:57:01: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:57:01: #1 total tags in treatment: 8546175 INFO @ Thu, 16 Apr 2020 05:57:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:57:01: #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 05:57:01: #1 tags after filtering in treatment: 8173093 INFO @ Thu, 16 Apr 2020 05:57:01: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:57:01: #1 finished! INFO @ Thu, 16 Apr 2020 05:57:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:57:01: 12000000 INFO @ Thu, 16 Apr 2020 05:57:01: #2 number of paired peaks: 998 WARNING @ Thu, 16 Apr 2020 05:57:01: Fewer paired peaks (998) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 998 pairs to build model! INFO @ Thu, 16 Apr 2020 05:57:01: start model_add_line... INFO @ Thu, 16 Apr 2020 05:57:02: 8000000 INFO @ Thu, 16 Apr 2020 05:57:02: start X-correlation... INFO @ Thu, 16 Apr 2020 05:57:02: end of X-cor INFO @ Thu, 16 Apr 2020 05:57:02: #2 finished! INFO @ Thu, 16 Apr 2020 05:57:02: #2 predicted fragment length is 171 bps INFO @ Thu, 16 Apr 2020 05:57:02: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 16 Apr 2020 05:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.05_model.r INFO @ Thu, 16 Apr 2020 05:57:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:57:09: 13000000 INFO @ Thu, 16 Apr 2020 05:57:10: 9000000 INFO @ Thu, 16 Apr 2020 05:57:17: 14000000 INFO @ Thu, 16 Apr 2020 05:57:18: 10000000 INFO @ Thu, 16 Apr 2020 05:57:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:57:24: 15000000 INFO @ Thu, 16 Apr 2020 05:57:26: 11000000 INFO @ Thu, 16 Apr 2020 05:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.05_summits.bed INFO @ Thu, 16 Apr 2020 05:57:27: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1870 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:57:32: 16000000 INFO @ Thu, 16 Apr 2020 05:57:35: 12000000 INFO @ Thu, 16 Apr 2020 05:57:41: 17000000 INFO @ Thu, 16 Apr 2020 05:57:43: 13000000 INFO @ Thu, 16 Apr 2020 05:57:46: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:57:46: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:57:46: #1 total tags in treatment: 8546175 INFO @ Thu, 16 Apr 2020 05:57:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:57:46: #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 05:57:46: #1 tags after filtering in treatment: 8173093 INFO @ Thu, 16 Apr 2020 05:57:46: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:57:46: #1 finished! INFO @ Thu, 16 Apr 2020 05:57:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:57:47: #2 number of paired peaks: 998 WARNING @ Thu, 16 Apr 2020 05:57:47: Fewer paired peaks (998) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 998 pairs to build model! INFO @ Thu, 16 Apr 2020 05:57:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:57:47: start X-correlation... INFO @ Thu, 16 Apr 2020 05:57:47: end of X-cor INFO @ Thu, 16 Apr 2020 05:57:47: #2 finished! INFO @ Thu, 16 Apr 2020 05:57:47: #2 predicted fragment length is 171 bps INFO @ Thu, 16 Apr 2020 05:57:47: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 16 Apr 2020 05:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.10_model.r INFO @ Thu, 16 Apr 2020 05:57:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:57:51: 14000000 INFO @ Thu, 16 Apr 2020 05:57:58: 15000000 INFO @ Thu, 16 Apr 2020 05:58:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:58:06: 16000000 INFO @ Thu, 16 Apr 2020 05:58:13: 17000000 INFO @ Thu, 16 Apr 2020 05:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.10_summits.bed INFO @ Thu, 16 Apr 2020 05:58:14: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1097 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:58:18: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:58:18: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:58:18: #1 total tags in treatment: 8546175 INFO @ Thu, 16 Apr 2020 05:58:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:58:18: #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 05:58:18: #1 tags after filtering in treatment: 8173093 INFO @ Thu, 16 Apr 2020 05:58:18: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:58:18: #1 finished! INFO @ Thu, 16 Apr 2020 05:58:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:58:18: #2 number of paired peaks: 998 WARNING @ Thu, 16 Apr 2020 05:58:18: Fewer paired peaks (998) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 998 pairs to build model! INFO @ Thu, 16 Apr 2020 05:58:18: start model_add_line... INFO @ Thu, 16 Apr 2020 05:58:19: start X-correlation... INFO @ Thu, 16 Apr 2020 05:58:19: end of X-cor INFO @ Thu, 16 Apr 2020 05:58:19: #2 finished! INFO @ Thu, 16 Apr 2020 05:58:19: #2 predicted fragment length is 171 bps INFO @ Thu, 16 Apr 2020 05:58:19: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 16 Apr 2020 05:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.20_model.r INFO @ Thu, 16 Apr 2020 05:58:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:58:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:58:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:58:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:58:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708286/SRX6708286.20_summits.bed INFO @ Thu, 16 Apr 2020 05:58:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。