Job ID = 5791274 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:20:41 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 ) 2020-04-22T00:20:41 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 ) 2020-04-22T00:28:08 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 ) 2020-04-22T00:29:22 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 : 21,712,071 reads read : 43,424,142 reads written : 43,424,142 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: 00:21:45 21712071 reads; of these: 21712071 (100.00%) were paired; of these: 16870215 (77.70%) aligned concordantly 0 times 1020721 (4.70%) aligned concordantly exactly 1 time 3821135 (17.60%) aligned concordantly >1 times ---- 16870215 pairs aligned concordantly 0 times; of these: 1004441 (5.95%) aligned discordantly 1 time ---- 15865774 pairs aligned 0 times concordantly or discordantly; of these: 31731548 mates make up the pairs; of these: 19924044 (62.79%) aligned 0 times 2972016 (9.37%) aligned exactly 1 time 8835488 (27.84%) aligned >1 times 54.12% overall alignment rate Time searching: 00:21:45 Overall time: 00:21:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 3820201 / 5621526 = 0.6796 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 @ Wed, 22 Apr 2020 09:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:57:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:57:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:57:23: 1000000 INFO @ Wed, 22 Apr 2020 09:57:27: 2000000 INFO @ Wed, 22 Apr 2020 09:57:32: 3000000 INFO @ Wed, 22 Apr 2020 09:57:37: 4000000 INFO @ Wed, 22 Apr 2020 09:57:42: 5000000 INFO @ Wed, 22 Apr 2020 09:57:46: 6000000 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 @ Wed, 22 Apr 2020 09:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:57:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:57:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:57:51: 7000000 INFO @ Wed, 22 Apr 2020 09:57:53: 1000000 INFO @ Wed, 22 Apr 2020 09:57:55: 8000000 INFO @ Wed, 22 Apr 2020 09:57:58: 2000000 INFO @ Wed, 22 Apr 2020 09:58:00: 9000000 INFO @ Wed, 22 Apr 2020 09:58:03: 3000000 INFO @ Wed, 22 Apr 2020 09:58:05: 10000000 INFO @ Wed, 22 Apr 2020 09:58:08: 4000000 INFO @ Wed, 22 Apr 2020 09:58:10: 11000000 INFO @ Wed, 22 Apr 2020 09:58:13: 5000000 INFO @ Wed, 22 Apr 2020 09:58:14: 12000000 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 @ Wed, 22 Apr 2020 09:58:18: 6000000 INFO @ Wed, 22 Apr 2020 09:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:58:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:58:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:58:19: 13000000 INFO @ Wed, 22 Apr 2020 09:58:23: 7000000 INFO @ Wed, 22 Apr 2020 09:58:24: 1000000 INFO @ Wed, 22 Apr 2020 09:58:24: 14000000 INFO @ Wed, 22 Apr 2020 09:58:27: 8000000 INFO @ Wed, 22 Apr 2020 09:58:28: 2000000 INFO @ Wed, 22 Apr 2020 09:58:28: 15000000 INFO @ Wed, 22 Apr 2020 09:58:32: 9000000 INFO @ Wed, 22 Apr 2020 09:58:32: 3000000 INFO @ Wed, 22 Apr 2020 09:58:32: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 09:58:32: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 09:58:32: #1 total tags in treatment: 1265051 INFO @ Wed, 22 Apr 2020 09:58:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:58:33: #1 tags after filtering in treatment: 294469 INFO @ Wed, 22 Apr 2020 09:58:33: #1 Redundant rate of treatment: 0.77 INFO @ Wed, 22 Apr 2020 09:58:33: #1 finished! INFO @ Wed, 22 Apr 2020 09:58:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:58:33: #2 number of paired peaks: 432 WARNING @ Wed, 22 Apr 2020 09:58:33: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Wed, 22 Apr 2020 09:58:33: start model_add_line... INFO @ Wed, 22 Apr 2020 09:58:33: start X-correlation... INFO @ Wed, 22 Apr 2020 09:58:33: end of X-cor INFO @ Wed, 22 Apr 2020 09:58:33: #2 finished! INFO @ Wed, 22 Apr 2020 09:58:33: #2 predicted fragment length is 191 bps INFO @ Wed, 22 Apr 2020 09:58:33: #2 alternative fragment length(s) may be 191 bps INFO @ Wed, 22 Apr 2020 09:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.05_model.r INFO @ Wed, 22 Apr 2020 09:58:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:58:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.05_summits.bed INFO @ Wed, 22 Apr 2020 09:58:34: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (402 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:58:37: 4000000 INFO @ Wed, 22 Apr 2020 09:58:37: 10000000 INFO @ Wed, 22 Apr 2020 09:58:41: 5000000 INFO @ Wed, 22 Apr 2020 09:58:42: 11000000 INFO @ Wed, 22 Apr 2020 09:58:45: 6000000 INFO @ Wed, 22 Apr 2020 09:58:47: 12000000 INFO @ Wed, 22 Apr 2020 09:58:49: 7000000 INFO @ Wed, 22 Apr 2020 09:58:51: 13000000 INFO @ Wed, 22 Apr 2020 09:58:53: 8000000 INFO @ Wed, 22 Apr 2020 09:58:56: 14000000 INFO @ Wed, 22 Apr 2020 09:58:57: 9000000 INFO @ Wed, 22 Apr 2020 09:59:01: 15000000 INFO @ Wed, 22 Apr 2020 09:59:02: 10000000 INFO @ Wed, 22 Apr 2020 09:59:05: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 09:59:05: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 09:59:05: #1 total tags in treatment: 1265051 INFO @ Wed, 22 Apr 2020 09:59:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:59:05: #1 tags after filtering in treatment: 294469 INFO @ Wed, 22 Apr 2020 09:59:05: #1 Redundant rate of treatment: 0.77 INFO @ Wed, 22 Apr 2020 09:59:05: #1 finished! INFO @ Wed, 22 Apr 2020 09:59:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:59:05: #2 number of paired peaks: 432 WARNING @ Wed, 22 Apr 2020 09:59:05: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Wed, 22 Apr 2020 09:59:05: start model_add_line... INFO @ Wed, 22 Apr 2020 09:59:05: start X-correlation... INFO @ Wed, 22 Apr 2020 09:59:05: end of X-cor INFO @ Wed, 22 Apr 2020 09:59:05: #2 finished! INFO @ Wed, 22 Apr 2020 09:59:05: #2 predicted fragment length is 191 bps INFO @ Wed, 22 Apr 2020 09:59:05: #2 alternative fragment length(s) may be 191 bps INFO @ Wed, 22 Apr 2020 09:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.10_model.r INFO @ Wed, 22 Apr 2020 09:59:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:59:06: 11000000 INFO @ Wed, 22 Apr 2020 09:59:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:59:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:59:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:59:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.10_summits.bed INFO @ Wed, 22 Apr 2020 09:59:07: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:59:10: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:59:14: 13000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:59:18: 14000000 INFO @ Wed, 22 Apr 2020 09:59:22: 15000000 INFO @ Wed, 22 Apr 2020 09:59:26: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 09:59:26: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 09:59:26: #1 total tags in treatment: 1265051 INFO @ Wed, 22 Apr 2020 09:59:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:59:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:59:26: #1 tags after filtering in treatment: 294469 INFO @ Wed, 22 Apr 2020 09:59:26: #1 Redundant rate of treatment: 0.77 INFO @ Wed, 22 Apr 2020 09:59:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:59:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:59:26: #2 number of paired peaks: 432 WARNING @ Wed, 22 Apr 2020 09:59:26: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Wed, 22 Apr 2020 09:59:26: start model_add_line... INFO @ Wed, 22 Apr 2020 09:59:26: start X-correlation... INFO @ Wed, 22 Apr 2020 09:59:26: end of X-cor INFO @ Wed, 22 Apr 2020 09:59:26: #2 finished! INFO @ Wed, 22 Apr 2020 09:59:26: #2 predicted fragment length is 191 bps INFO @ Wed, 22 Apr 2020 09:59:26: #2 alternative fragment length(s) may be 191 bps INFO @ Wed, 22 Apr 2020 09:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.20_model.r INFO @ Wed, 22 Apr 2020 09:59:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:59:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:59:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:59:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:59:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7399906/SRX7399906.20_summits.bed INFO @ Wed, 22 Apr 2020 09:59:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 1 millis CompletedMACS2peakCalling