Job ID = 5721179 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,414,500 reads read : 22,829,000 reads written : 22,829,000 spots read : 11,359,144 reads read : 22,718,288 reads written : 22,718,288 2020-04-15T20:42:44 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 ) 2020-04-15T20:42:44 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 : 11,176,110 reads read : 22,352,220 reads written : 22,352,220 spots read : 11,212,063 reads read : 22,424,126 reads written : 22,424,126 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: 00:14:35 45161817 reads; of these: 45161817 (100.00%) were paired; of these: 39326196 (87.08%) aligned concordantly 0 times 4537232 (10.05%) aligned concordantly exactly 1 time 1298389 (2.87%) aligned concordantly >1 times ---- 39326196 pairs aligned concordantly 0 times; of these: 22419 (0.06%) aligned discordantly 1 time ---- 39303777 pairs aligned 0 times concordantly or discordantly; of these: 78607554 mates make up the pairs; of these: 77071495 (98.05%) aligned 0 times 596685 (0.76%) aligned exactly 1 time 939374 (1.20%) aligned >1 times 14.67% overall alignment rate Time searching: 00:14:35 Overall time: 00:14:35 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_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] 244643 / 5843715 = 0.0419 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 06:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.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 06:13:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:13:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:13:43: 1000000 INFO @ Thu, 16 Apr 2020 06:13:49: 2000000 INFO @ Thu, 16 Apr 2020 06:13:54: 3000000 INFO @ Thu, 16 Apr 2020 06:13:59: 4000000 INFO @ Thu, 16 Apr 2020 06:14:05: 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 06:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.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 06:14:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:14:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:14:10: 6000000 INFO @ Thu, 16 Apr 2020 06:14:13: 1000000 INFO @ Thu, 16 Apr 2020 06:14:15: 7000000 INFO @ Thu, 16 Apr 2020 06:14:17: 2000000 INFO @ Thu, 16 Apr 2020 06:14:21: 8000000 INFO @ Thu, 16 Apr 2020 06:14:22: 3000000 INFO @ Thu, 16 Apr 2020 06:14:27: 9000000 INFO @ Thu, 16 Apr 2020 06:14:27: 4000000 INFO @ Thu, 16 Apr 2020 06:14:32: 5000000 INFO @ Thu, 16 Apr 2020 06:14:32: 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 06:14:37: 6000000 INFO @ Thu, 16 Apr 2020 06:14:37: 11000000 INFO @ Thu, 16 Apr 2020 06:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.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 06:14:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:14:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:14:41: 7000000 INFO @ Thu, 16 Apr 2020 06:14:43: 12000000 INFO @ Thu, 16 Apr 2020 06:14:43: 1000000 INFO @ Thu, 16 Apr 2020 06:14:46: 8000000 INFO @ Thu, 16 Apr 2020 06:14:47: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:14:47: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:14:47: #1 total tags in treatment: 5591136 INFO @ Thu, 16 Apr 2020 06:14:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:14:47: #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 06:14:47: #1 tags after filtering in treatment: 4748831 INFO @ Thu, 16 Apr 2020 06:14:47: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:14:47: #1 finished! INFO @ Thu, 16 Apr 2020 06:14:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:14:47: #2 number of paired peaks: 4713 INFO @ Thu, 16 Apr 2020 06:14:47: start model_add_line... INFO @ Thu, 16 Apr 2020 06:14:47: 2000000 INFO @ Thu, 16 Apr 2020 06:14:47: start X-correlation... INFO @ Thu, 16 Apr 2020 06:14:48: end of X-cor INFO @ Thu, 16 Apr 2020 06:14:48: #2 finished! INFO @ Thu, 16 Apr 2020 06:14:48: #2 predicted fragment length is 148 bps INFO @ Thu, 16 Apr 2020 06:14:48: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 16 Apr 2020 06:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.05_model.r INFO @ Thu, 16 Apr 2020 06:14:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:14:51: 9000000 INFO @ Thu, 16 Apr 2020 06:14:52: 3000000 INFO @ Thu, 16 Apr 2020 06:14:56: 10000000 INFO @ Thu, 16 Apr 2020 06:14:57: 4000000 INFO @ Thu, 16 Apr 2020 06:15:00: 11000000 INFO @ Thu, 16 Apr 2020 06:15:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:15:01: 5000000 INFO @ Thu, 16 Apr 2020 06:15:04: 12000000 INFO @ Thu, 16 Apr 2020 06:15:06: 6000000 INFO @ Thu, 16 Apr 2020 06:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.05_summits.bed INFO @ Thu, 16 Apr 2020 06:15:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6666 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:15:08: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:15:08: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:15:08: #1 total tags in treatment: 5591136 INFO @ Thu, 16 Apr 2020 06:15:08: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:15:08: #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 06:15:08: #1 tags after filtering in treatment: 4748831 INFO @ Thu, 16 Apr 2020 06:15:08: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:15:08: #1 finished! INFO @ Thu, 16 Apr 2020 06:15:08: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:15:09: #2 number of paired peaks: 4713 INFO @ Thu, 16 Apr 2020 06:15:09: start model_add_line... INFO @ Thu, 16 Apr 2020 06:15:09: start X-correlation... INFO @ Thu, 16 Apr 2020 06:15:09: end of X-cor INFO @ Thu, 16 Apr 2020 06:15:09: #2 finished! INFO @ Thu, 16 Apr 2020 06:15:09: #2 predicted fragment length is 148 bps INFO @ Thu, 16 Apr 2020 06:15:09: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 16 Apr 2020 06:15:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.10_model.r INFO @ Thu, 16 Apr 2020 06:15:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:15:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:15:10: 7000000 INFO @ Thu, 16 Apr 2020 06:15:15: 8000000 INFO @ Thu, 16 Apr 2020 06:15:19: 9000000 INFO @ Thu, 16 Apr 2020 06:15:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:15:24: 10000000 INFO @ Thu, 16 Apr 2020 06:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.10_summits.bed INFO @ Thu, 16 Apr 2020 06:15:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2895 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:15:28: 11000000 INFO @ Thu, 16 Apr 2020 06:15:32: 12000000 INFO @ Thu, 16 Apr 2020 06:15:35: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:15:35: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:15:35: #1 total tags in treatment: 5591136 INFO @ Thu, 16 Apr 2020 06:15:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:15:35: #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 06:15:35: #1 tags after filtering in treatment: 4748831 INFO @ Thu, 16 Apr 2020 06:15:35: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:15:35: #1 finished! INFO @ Thu, 16 Apr 2020 06:15:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:15:36: #2 number of paired peaks: 4713 INFO @ Thu, 16 Apr 2020 06:15:36: start model_add_line... INFO @ Thu, 16 Apr 2020 06:15:36: start X-correlation... INFO @ Thu, 16 Apr 2020 06:15:36: end of X-cor INFO @ Thu, 16 Apr 2020 06:15:36: #2 finished! INFO @ Thu, 16 Apr 2020 06:15:36: #2 predicted fragment length is 148 bps INFO @ Thu, 16 Apr 2020 06:15:36: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 16 Apr 2020 06:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.20_model.r INFO @ Thu, 16 Apr 2020 06:15:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:15:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762288/SRX6762288.20_summits.bed INFO @ Thu, 16 Apr 2020 06:15:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (829 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。