Job ID = 5721109 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:41:34 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 ) 2020-04-15T19:41:34 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 : 7,859,407 reads read : 15,718,814 reads written : 15,718,814 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: 00:00:01 Multiseed full-index search: 00:12:07 7859407 reads; of these: 7859407 (100.00%) were paired; of these: 1038365 (13.21%) aligned concordantly 0 times 5407031 (68.80%) aligned concordantly exactly 1 time 1414011 (17.99%) aligned concordantly >1 times ---- 1038365 pairs aligned concordantly 0 times; of these: 291890 (28.11%) aligned discordantly 1 time ---- 746475 pairs aligned 0 times concordantly or discordantly; of these: 1492950 mates make up the pairs; of these: 947582 (63.47%) aligned 0 times 245048 (16.41%) aligned exactly 1 time 300320 (20.12%) aligned >1 times 93.97% overall alignment rate Time searching: 00:12:08 Overall time: 00:12:08 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] 644910 / 7097301 = 0.0909 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 05:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.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 05:04:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:04:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:04:09: 1000000 INFO @ Thu, 16 Apr 2020 05:04:15: 2000000 INFO @ Thu, 16 Apr 2020 05:04:21: 3000000 INFO @ Thu, 16 Apr 2020 05:04:27: 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 05:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.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 05:04:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:04:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:04:33: 5000000 INFO @ Thu, 16 Apr 2020 05:04:38: 1000000 INFO @ Thu, 16 Apr 2020 05:04:40: 6000000 INFO @ Thu, 16 Apr 2020 05:04:45: 2000000 INFO @ Thu, 16 Apr 2020 05:04:47: 7000000 INFO @ Thu, 16 Apr 2020 05:04:52: 3000000 INFO @ Thu, 16 Apr 2020 05:04:53: 8000000 INFO @ Thu, 16 Apr 2020 05:04:58: 4000000 BedGraph に変換中... INFO @ Thu, 16 Apr 2020 05:05:00: 9000000 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 05:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.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 05:05:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:05:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:05:05: 5000000 INFO @ Thu, 16 Apr 2020 05:05:07: 10000000 INFO @ Thu, 16 Apr 2020 05:05:10: 1000000 INFO @ Thu, 16 Apr 2020 05:05:12: 6000000 INFO @ Thu, 16 Apr 2020 05:05:14: 11000000 INFO @ Thu, 16 Apr 2020 05:05:17: 2000000 INFO @ Thu, 16 Apr 2020 05:05:19: 7000000 INFO @ Thu, 16 Apr 2020 05:05:21: 12000000 INFO @ Thu, 16 Apr 2020 05:05:25: 3000000 INFO @ Thu, 16 Apr 2020 05:05:27: 8000000 INFO @ Thu, 16 Apr 2020 05:05:28: 13000000 INFO @ Thu, 16 Apr 2020 05:05:31: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:05:31: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:05:31: #1 total tags in treatment: 6197716 INFO @ Thu, 16 Apr 2020 05:05:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:05:31: #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 05:05:32: #1 tags after filtering in treatment: 5774918 INFO @ Thu, 16 Apr 2020 05:05:32: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:05:32: #1 finished! INFO @ Thu, 16 Apr 2020 05:05:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:05:32: #2 number of paired peaks: 598 WARNING @ Thu, 16 Apr 2020 05:05:32: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Thu, 16 Apr 2020 05:05:32: start model_add_line... INFO @ Thu, 16 Apr 2020 05:05:32: start X-correlation... INFO @ Thu, 16 Apr 2020 05:05:32: end of X-cor INFO @ Thu, 16 Apr 2020 05:05:32: #2 finished! INFO @ Thu, 16 Apr 2020 05:05:32: #2 predicted fragment length is 193 bps INFO @ Thu, 16 Apr 2020 05:05:32: #2 alternative fragment length(s) may be 193 bps INFO @ Thu, 16 Apr 2020 05:05:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.05_model.r INFO @ Thu, 16 Apr 2020 05:05:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:05:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:05:33: 4000000 INFO @ Thu, 16 Apr 2020 05:05:34: 9000000 INFO @ Thu, 16 Apr 2020 05:05:41: 10000000 INFO @ Thu, 16 Apr 2020 05:05:42: 5000000 INFO @ Thu, 16 Apr 2020 05:05:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:05:48: 11000000 INFO @ Thu, 16 Apr 2020 05:05:50: 6000000 INFO @ Thu, 16 Apr 2020 05:05:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:05:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:05:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.05_summits.bed INFO @ Thu, 16 Apr 2020 05:05:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2622 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:05:55: 12000000 INFO @ Thu, 16 Apr 2020 05:05:58: 7000000 INFO @ Thu, 16 Apr 2020 05:06:02: 13000000 INFO @ Thu, 16 Apr 2020 05:06:05: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:06:05: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:06:05: #1 total tags in treatment: 6197716 INFO @ Thu, 16 Apr 2020 05:06:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:06:05: #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 05:06:05: #1 tags after filtering in treatment: 5774918 INFO @ Thu, 16 Apr 2020 05:06:05: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:06:05: #1 finished! INFO @ Thu, 16 Apr 2020 05:06:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:06:06: 8000000 INFO @ Thu, 16 Apr 2020 05:06:06: #2 number of paired peaks: 598 WARNING @ Thu, 16 Apr 2020 05:06:06: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Thu, 16 Apr 2020 05:06:06: start model_add_line... INFO @ Thu, 16 Apr 2020 05:06:06: start X-correlation... INFO @ Thu, 16 Apr 2020 05:06:06: end of X-cor INFO @ Thu, 16 Apr 2020 05:06:06: #2 finished! INFO @ Thu, 16 Apr 2020 05:06:06: #2 predicted fragment length is 193 bps INFO @ Thu, 16 Apr 2020 05:06:06: #2 alternative fragment length(s) may be 193 bps INFO @ Thu, 16 Apr 2020 05:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.10_model.r INFO @ Thu, 16 Apr 2020 05:06:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:06:14: 9000000 INFO @ Thu, 16 Apr 2020 05:06:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:06:22: 10000000 INFO @ Thu, 16 Apr 2020 05:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.10_summits.bed INFO @ Thu, 16 Apr 2020 05:06:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1127 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:06:30: 11000000 INFO @ Thu, 16 Apr 2020 05:06:38: 12000000 INFO @ Thu, 16 Apr 2020 05:06:46: 13000000 INFO @ Thu, 16 Apr 2020 05:06:49: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:06:49: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:06:49: #1 total tags in treatment: 6197716 INFO @ Thu, 16 Apr 2020 05:06:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:06:49: #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 05:06:49: #1 tags after filtering in treatment: 5774918 INFO @ Thu, 16 Apr 2020 05:06:49: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:06:49: #1 finished! INFO @ Thu, 16 Apr 2020 05:06:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:06:50: #2 number of paired peaks: 598 WARNING @ Thu, 16 Apr 2020 05:06:50: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Thu, 16 Apr 2020 05:06:50: start model_add_line... INFO @ Thu, 16 Apr 2020 05:06:50: start X-correlation... INFO @ Thu, 16 Apr 2020 05:06:50: end of X-cor INFO @ Thu, 16 Apr 2020 05:06:50: #2 finished! INFO @ Thu, 16 Apr 2020 05:06:50: #2 predicted fragment length is 193 bps INFO @ Thu, 16 Apr 2020 05:06:50: #2 alternative fragment length(s) may be 193 bps INFO @ Thu, 16 Apr 2020 05:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.20_model.r INFO @ Thu, 16 Apr 2020 05:06:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:07:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708253/SRX6708253.20_summits.bed INFO @ Thu, 16 Apr 2020 05:07:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (442 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。