Job ID = 5790951 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:06:25 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 ) 2020-04-21T23:06:25 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 ) 2020-04-21T23:07:13 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 ) 2020-04-21T23:08:34 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 : 2,613,770 reads read : 5,227,540 reads written : 5,227,540 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: 00:01:55 2613770 reads; of these: 2613770 (100.00%) were paired; of these: 132595 (5.07%) aligned concordantly 0 times 1748522 (66.90%) aligned concordantly exactly 1 time 732653 (28.03%) aligned concordantly >1 times ---- 132595 pairs aligned concordantly 0 times; of these: 1122 (0.85%) aligned discordantly 1 time ---- 131473 pairs aligned 0 times concordantly or discordantly; of these: 262946 mates make up the pairs; of these: 242688 (92.30%) aligned 0 times 11837 (4.50%) aligned exactly 1 time 8421 (3.20%) aligned >1 times 95.36% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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_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] 148820 / 2466777 = 0.0603 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 08:13:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.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 08:13:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:52: 1000000 INFO @ Wed, 22 Apr 2020 08:13:57: 2000000 INFO @ Wed, 22 Apr 2020 08:14:02: 3000000 INFO @ Wed, 22 Apr 2020 08:14:07: 4000000 INFO @ Wed, 22 Apr 2020 08:14:11: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:11: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:11: #1 total tags in treatment: 2332358 INFO @ Wed, 22 Apr 2020 08:14:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:11: #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 08:14:11: #1 tags after filtering in treatment: 1838410 INFO @ Wed, 22 Apr 2020 08:14:11: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:14:11: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:11: #2 number of paired peaks: 187 WARNING @ Wed, 22 Apr 2020 08:14:11: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:11: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:11: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:11: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:11: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:11: #2 predicted fragment length is 110 bps INFO @ Wed, 22 Apr 2020 08:14:11: #2 alternative fragment length(s) may be 2,90,110,597 bps INFO @ Wed, 22 Apr 2020 08:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.05_model.r WARNING @ Wed, 22 Apr 2020 08:14:11: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:14:11: #2 You may need to consider one of the other alternative d(s): 2,90,110,597 WARNING @ Wed, 22 Apr 2020 08:14:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:14:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:11: #3 Pre-compute pvalue-qvalue table... 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 08:14:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.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 08:14:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:14:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.05_summits.bed INFO @ Wed, 22 Apr 2020 08:14:17: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (503 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:14:22: 1000000 INFO @ Wed, 22 Apr 2020 08:14:28: 2000000 INFO @ Wed, 22 Apr 2020 08:14:33: 3000000 INFO @ Wed, 22 Apr 2020 08:14:39: 4000000 INFO @ Wed, 22 Apr 2020 08:14:42: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:42: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:42: #1 total tags in treatment: 2332358 INFO @ Wed, 22 Apr 2020 08:14:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:42: #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 08:14:42: #1 tags after filtering in treatment: 1838410 INFO @ Wed, 22 Apr 2020 08:14:42: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:14:42: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:42: #2 number of paired peaks: 187 WARNING @ Wed, 22 Apr 2020 08:14:42: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:42: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:42: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:42: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:42: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:42: #2 predicted fragment length is 110 bps INFO @ Wed, 22 Apr 2020 08:14:42: #2 alternative fragment length(s) may be 2,90,110,597 bps INFO @ Wed, 22 Apr 2020 08:14:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.10_model.r WARNING @ Wed, 22 Apr 2020 08:14:42: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:14:42: #2 You may need to consider one of the other alternative d(s): 2,90,110,597 WARNING @ Wed, 22 Apr 2020 08:14:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:14:42: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:42: #3 Pre-compute pvalue-qvalue table... 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 08:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.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 08:14:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:14:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.10_summits.bed INFO @ Wed, 22 Apr 2020 08:14:49: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (307 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:14:52: 1000000 INFO @ Wed, 22 Apr 2020 08:14:57: 2000000 INFO @ Wed, 22 Apr 2020 08:15:03: 3000000 INFO @ Wed, 22 Apr 2020 08:15:08: 4000000 INFO @ Wed, 22 Apr 2020 08:15:12: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:12: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:12: #1 total tags in treatment: 2332358 INFO @ Wed, 22 Apr 2020 08:15:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:12: #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 08:15:12: #1 tags after filtering in treatment: 1838410 INFO @ Wed, 22 Apr 2020 08:15:12: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:15:12: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:12: #2 number of paired peaks: 187 WARNING @ Wed, 22 Apr 2020 08:15:12: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:12: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:12: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:12: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:12: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:12: #2 predicted fragment length is 110 bps INFO @ Wed, 22 Apr 2020 08:15:12: #2 alternative fragment length(s) may be 2,90,110,597 bps INFO @ Wed, 22 Apr 2020 08:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.20_model.r WARNING @ Wed, 22 Apr 2020 08:15:12: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:15:12: #2 You may need to consider one of the other alternative d(s): 2,90,110,597 WARNING @ Wed, 22 Apr 2020 08:15:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:15:12: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:15:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874466/SRX5874466.20_summits.bed INFO @ Wed, 22 Apr 2020 08:15:18: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (130 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。