Job ID = 5721099 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:33:42 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 ) 2020-04-15T19:33:42 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 ) 2020-04-15T19:33:42 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 : 11,560,479 reads read : 23,120,958 reads written : 23,120,958 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: 00:25:46 11560479 reads; of these: 11560479 (100.00%) were paired; of these: 1014896 (8.78%) aligned concordantly 0 times 7290554 (63.06%) aligned concordantly exactly 1 time 3255029 (28.16%) aligned concordantly >1 times ---- 1014896 pairs aligned concordantly 0 times; of these: 306918 (30.24%) aligned discordantly 1 time ---- 707978 pairs aligned 0 times concordantly or discordantly; of these: 1415956 mates make up the pairs; of these: 813972 (57.49%) aligned 0 times 307695 (21.73%) aligned exactly 1 time 294289 (20.78%) aligned >1 times 96.48% overall alignment rate Time searching: 00:25:46 Overall time: 00:25:46 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 12 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] 1028675 / 10782046 = 0.0954 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 05:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.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 05:14:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:14:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:14:22: 1000000 INFO @ Thu, 16 Apr 2020 05:14:28: 2000000 INFO @ Thu, 16 Apr 2020 05:14:33: 3000000 INFO @ Thu, 16 Apr 2020 05:14:38: 4000000 INFO @ Thu, 16 Apr 2020 05:14:43: 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 05:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.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 05:14:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:14:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:14:49: 6000000 INFO @ Thu, 16 Apr 2020 05:14:53: 1000000 INFO @ Thu, 16 Apr 2020 05:14:54: 7000000 INFO @ Thu, 16 Apr 2020 05:14:59: 2000000 INFO @ Thu, 16 Apr 2020 05:15:00: 8000000 INFO @ Thu, 16 Apr 2020 05:15:04: 3000000 INFO @ Thu, 16 Apr 2020 05:15:06: 9000000 INFO @ Thu, 16 Apr 2020 05:15:10: 4000000 INFO @ Thu, 16 Apr 2020 05:15:12: 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 05:15:16: 5000000 INFO @ Thu, 16 Apr 2020 05:15:17: 11000000 INFO @ Thu, 16 Apr 2020 05:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.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 05:15:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:15:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:15:21: 6000000 INFO @ Thu, 16 Apr 2020 05:15:23: 12000000 INFO @ Thu, 16 Apr 2020 05:15:23: 1000000 INFO @ Thu, 16 Apr 2020 05:15:27: 7000000 INFO @ Thu, 16 Apr 2020 05:15:29: 13000000 INFO @ Thu, 16 Apr 2020 05:15:29: 2000000 INFO @ Thu, 16 Apr 2020 05:15:33: 8000000 INFO @ Thu, 16 Apr 2020 05:15:35: 14000000 INFO @ Thu, 16 Apr 2020 05:15:35: 3000000 INFO @ Thu, 16 Apr 2020 05:15:39: 9000000 INFO @ Thu, 16 Apr 2020 05:15:40: 15000000 INFO @ Thu, 16 Apr 2020 05:15:41: 4000000 INFO @ Thu, 16 Apr 2020 05:15:45: 10000000 INFO @ Thu, 16 Apr 2020 05:15:46: 16000000 INFO @ Thu, 16 Apr 2020 05:15:46: 5000000 INFO @ Thu, 16 Apr 2020 05:15:50: 11000000 INFO @ Thu, 16 Apr 2020 05:15:52: 17000000 INFO @ Thu, 16 Apr 2020 05:15:52: 6000000 INFO @ Thu, 16 Apr 2020 05:15:56: 12000000 INFO @ Thu, 16 Apr 2020 05:15:58: 18000000 INFO @ Thu, 16 Apr 2020 05:15:58: 7000000 INFO @ Thu, 16 Apr 2020 05:16:02: 13000000 INFO @ Thu, 16 Apr 2020 05:16:03: 19000000 INFO @ Thu, 16 Apr 2020 05:16:04: 8000000 INFO @ Thu, 16 Apr 2020 05:16:07: 14000000 INFO @ Thu, 16 Apr 2020 05:16:09: 20000000 INFO @ Thu, 16 Apr 2020 05:16:10: 9000000 INFO @ Thu, 16 Apr 2020 05:16:11: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:16:11: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:16:11: #1 total tags in treatment: 9528384 INFO @ Thu, 16 Apr 2020 05:16:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:16:11: #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 05:16:11: #1 tags after filtering in treatment: 8917368 INFO @ Thu, 16 Apr 2020 05:16:11: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:16:11: #1 finished! INFO @ Thu, 16 Apr 2020 05:16:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:16:11: #2 number of paired peaks: 718 WARNING @ Thu, 16 Apr 2020 05:16:11: Fewer paired peaks (718) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 718 pairs to build model! INFO @ Thu, 16 Apr 2020 05:16:11: start model_add_line... INFO @ Thu, 16 Apr 2020 05:16:11: start X-correlation... INFO @ Thu, 16 Apr 2020 05:16:11: end of X-cor INFO @ Thu, 16 Apr 2020 05:16:11: #2 finished! INFO @ Thu, 16 Apr 2020 05:16:11: #2 predicted fragment length is 169 bps INFO @ Thu, 16 Apr 2020 05:16:11: #2 alternative fragment length(s) may be 169 bps INFO @ Thu, 16 Apr 2020 05:16:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.05_model.r INFO @ Thu, 16 Apr 2020 05:16:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:16:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:16:13: 15000000 INFO @ Thu, 16 Apr 2020 05:16:15: 10000000 INFO @ Thu, 16 Apr 2020 05:16:19: 16000000 INFO @ Thu, 16 Apr 2020 05:16:21: 11000000 INFO @ Thu, 16 Apr 2020 05:16:25: 17000000 INFO @ Thu, 16 Apr 2020 05:16:27: 12000000 INFO @ Thu, 16 Apr 2020 05:16:30: 18000000 INFO @ Thu, 16 Apr 2020 05:16:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:16:32: 13000000 INFO @ Thu, 16 Apr 2020 05:16:36: 19000000 INFO @ Thu, 16 Apr 2020 05:16:38: 14000000 INFO @ Thu, 16 Apr 2020 05:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.05_summits.bed INFO @ Thu, 16 Apr 2020 05:16:39: Done! INFO @ Thu, 16 Apr 2020 05:16:42: 20000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1992 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:16:43: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:16:43: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:16:43: #1 total tags in treatment: 9528384 INFO @ Thu, 16 Apr 2020 05:16:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:16:43: #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 05:16:43: #1 tags after filtering in treatment: 8917368 INFO @ Thu, 16 Apr 2020 05:16:43: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:16:43: #1 finished! INFO @ Thu, 16 Apr 2020 05:16:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:16:44: 15000000 INFO @ Thu, 16 Apr 2020 05:16:44: #2 number of paired peaks: 718 WARNING @ Thu, 16 Apr 2020 05:16:44: Fewer paired peaks (718) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 718 pairs to build model! INFO @ Thu, 16 Apr 2020 05:16:44: start model_add_line... INFO @ Thu, 16 Apr 2020 05:16:44: start X-correlation... INFO @ Thu, 16 Apr 2020 05:16:44: end of X-cor INFO @ Thu, 16 Apr 2020 05:16:44: #2 finished! INFO @ Thu, 16 Apr 2020 05:16:44: #2 predicted fragment length is 169 bps INFO @ Thu, 16 Apr 2020 05:16:44: #2 alternative fragment length(s) may be 169 bps INFO @ Thu, 16 Apr 2020 05:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.10_model.r INFO @ Thu, 16 Apr 2020 05:16:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:16:49: 16000000 INFO @ Thu, 16 Apr 2020 05:16:55: 17000000 INFO @ Thu, 16 Apr 2020 05:17:00: 18000000 INFO @ Thu, 16 Apr 2020 05:17:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:17:06: 19000000 INFO @ Thu, 16 Apr 2020 05:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.10_summits.bed INFO @ Thu, 16 Apr 2020 05:17:11: Done! INFO @ Thu, 16 Apr 2020 05:17:11: 20000000 INFO @ Thu, 16 Apr 2020 05:17:13: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:17:13: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:17:13: #1 total tags in treatment: 9528384 INFO @ Thu, 16 Apr 2020 05:17:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:17:13: #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 05:17:13: #1 tags after filtering in treatment: 8917368 INFO @ Thu, 16 Apr 2020 05:17:13: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:17:13: #1 finished! INFO @ Thu, 16 Apr 2020 05:17:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:17:13: #2 number of paired peaks: 718 WARNING @ Thu, 16 Apr 2020 05:17:13: Fewer paired peaks (718) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 718 pairs to build model! INFO @ Thu, 16 Apr 2020 05:17:13: start model_add_line... INFO @ Thu, 16 Apr 2020 05:17:14: start X-correlation... INFO @ Thu, 16 Apr 2020 05:17:14: end of X-cor INFO @ Thu, 16 Apr 2020 05:17:14: #2 finished! INFO @ Thu, 16 Apr 2020 05:17:14: #2 predicted fragment length is 169 bps INFO @ Thu, 16 Apr 2020 05:17:14: #2 alternative fragment length(s) may be 169 bps INFO @ Thu, 16 Apr 2020 05:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.20_model.r INFO @ Thu, 16 Apr 2020 05:17:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:17:14: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1177 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:17:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708245/SRX6708245.20_summits.bed INFO @ Thu, 16 Apr 2020 05:17:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (614 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。