Job ID = 5721107 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:44:06 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 : 9,064,187 reads read : 18,128,374 reads written : 18,128,374 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: 00:18:12 9064187 reads; of these: 9064187 (100.00%) were paired; of these: 930358 (10.26%) aligned concordantly 0 times 5913453 (65.24%) aligned concordantly exactly 1 time 2220376 (24.50%) aligned concordantly >1 times ---- 930358 pairs aligned concordantly 0 times; of these: 324507 (34.88%) aligned discordantly 1 time ---- 605851 pairs aligned 0 times concordantly or discordantly; of these: 1211702 mates make up the pairs; of these: 624574 (51.55%) aligned 0 times 305696 (25.23%) aligned exactly 1 time 281432 (23.23%) aligned >1 times 96.55% overall alignment rate Time searching: 00:18:12 Overall time: 00:18:12 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] 634778 / 8419019 = 0.0754 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 05:10:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.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 05:10:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:10:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:10:21: 1000000 INFO @ Thu, 16 Apr 2020 05:10:27: 2000000 INFO @ Thu, 16 Apr 2020 05:10:32: 3000000 INFO @ Thu, 16 Apr 2020 05:10:37: 4000000 INFO @ Thu, 16 Apr 2020 05:10:43: 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 05:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.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 05:10:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:10:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:10:48: 6000000 INFO @ Thu, 16 Apr 2020 05:10:52: 1000000 INFO @ Thu, 16 Apr 2020 05:10:54: 7000000 INFO @ Thu, 16 Apr 2020 05:10:58: 2000000 INFO @ Thu, 16 Apr 2020 05:11:00: 8000000 INFO @ Thu, 16 Apr 2020 05:11:04: 3000000 INFO @ Thu, 16 Apr 2020 05:11:06: 9000000 INFO @ Thu, 16 Apr 2020 05:11:10: 4000000 INFO @ Thu, 16 Apr 2020 05:11:12: 10000000 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 05:11:16: 5000000 INFO @ Thu, 16 Apr 2020 05:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.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 05:11:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:11:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:11:18: 11000000 INFO @ Thu, 16 Apr 2020 05:11:22: 6000000 INFO @ Thu, 16 Apr 2020 05:11:22: 1000000 INFO @ Thu, 16 Apr 2020 05:11:24: 12000000 INFO @ Thu, 16 Apr 2020 05:11:28: 7000000 INFO @ Thu, 16 Apr 2020 05:11:28: 2000000 INFO @ Thu, 16 Apr 2020 05:11:30: 13000000 INFO @ Thu, 16 Apr 2020 05:11:34: 8000000 INFO @ Thu, 16 Apr 2020 05:11:34: 3000000 INFO @ Thu, 16 Apr 2020 05:11:36: 14000000 INFO @ Thu, 16 Apr 2020 05:11:40: 9000000 INFO @ Thu, 16 Apr 2020 05:11:40: 4000000 INFO @ Thu, 16 Apr 2020 05:11:42: 15000000 INFO @ Thu, 16 Apr 2020 05:11:46: 10000000 INFO @ Thu, 16 Apr 2020 05:11:46: 5000000 INFO @ Thu, 16 Apr 2020 05:11:48: 16000000 INFO @ Thu, 16 Apr 2020 05:11:50: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:11:50: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:11:50: #1 total tags in treatment: 7513120 INFO @ Thu, 16 Apr 2020 05:11:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:50: #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 05:11:50: #1 tags after filtering in treatment: 7098833 INFO @ Thu, 16 Apr 2020 05:11:50: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:11:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:50: #2 number of paired peaks: 1065 INFO @ Thu, 16 Apr 2020 05:11:50: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:50: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:50: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:50: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:50: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 05:11:50: #2 alternative fragment length(s) may be 196 bps INFO @ Thu, 16 Apr 2020 05:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.05_model.r INFO @ Thu, 16 Apr 2020 05:11:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:52: 11000000 INFO @ Thu, 16 Apr 2020 05:11:52: 6000000 INFO @ Thu, 16 Apr 2020 05:11:58: 12000000 INFO @ Thu, 16 Apr 2020 05:11:58: 7000000 INFO @ Thu, 16 Apr 2020 05:12:03: 13000000 INFO @ Thu, 16 Apr 2020 05:12:04: 8000000 INFO @ Thu, 16 Apr 2020 05:12:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:12:09: 14000000 INFO @ Thu, 16 Apr 2020 05:12:10: 9000000 INFO @ Thu, 16 Apr 2020 05:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.05_summits.bed INFO @ Thu, 16 Apr 2020 05:12:15: Done! INFO @ Thu, 16 Apr 2020 05:12:15: 15000000 INFO @ Thu, 16 Apr 2020 05:12:15: 10000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1596 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:12:21: 16000000 INFO @ Thu, 16 Apr 2020 05:12:21: 11000000 INFO @ Thu, 16 Apr 2020 05:12:23: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:12:23: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:12:23: #1 total tags in treatment: 7513120 INFO @ Thu, 16 Apr 2020 05:12:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:12:23: #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 05:12:23: #1 tags after filtering in treatment: 7098833 INFO @ Thu, 16 Apr 2020 05:12:23: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:12:23: #1 finished! INFO @ Thu, 16 Apr 2020 05:12:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:12:23: #2 number of paired peaks: 1065 INFO @ Thu, 16 Apr 2020 05:12:23: start model_add_line... INFO @ Thu, 16 Apr 2020 05:12:23: start X-correlation... INFO @ Thu, 16 Apr 2020 05:12:23: end of X-cor INFO @ Thu, 16 Apr 2020 05:12:23: #2 finished! INFO @ Thu, 16 Apr 2020 05:12:23: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 05:12:23: #2 alternative fragment length(s) may be 196 bps INFO @ Thu, 16 Apr 2020 05:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.10_model.r INFO @ Thu, 16 Apr 2020 05:12:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:12:27: 12000000 INFO @ Thu, 16 Apr 2020 05:12:33: 13000000 INFO @ Thu, 16 Apr 2020 05:12:38: 14000000 INFO @ Thu, 16 Apr 2020 05:12:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:12:44: 15000000 INFO @ Thu, 16 Apr 2020 05:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.10_summits.bed INFO @ Thu, 16 Apr 2020 05:12:47: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (970 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:12:50: 16000000 INFO @ Thu, 16 Apr 2020 05:12:51: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:12:51: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:12:51: #1 total tags in treatment: 7513120 INFO @ Thu, 16 Apr 2020 05:12:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:12:51: #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 05:12:51: #1 tags after filtering in treatment: 7098833 INFO @ Thu, 16 Apr 2020 05:12:51: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:12:51: #1 finished! INFO @ Thu, 16 Apr 2020 05:12:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:12:52: #2 number of paired peaks: 1065 INFO @ Thu, 16 Apr 2020 05:12:52: start model_add_line... INFO @ Thu, 16 Apr 2020 05:12:52: start X-correlation... INFO @ Thu, 16 Apr 2020 05:12:52: end of X-cor INFO @ Thu, 16 Apr 2020 05:12:52: #2 finished! INFO @ Thu, 16 Apr 2020 05:12:52: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 05:12:52: #2 alternative fragment length(s) may be 196 bps INFO @ Thu, 16 Apr 2020 05:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.20_model.r INFO @ Thu, 16 Apr 2020 05:12:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:13:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708251/SRX6708251.20_summits.bed INFO @ Thu, 16 Apr 2020 05:13:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (484 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。