Job ID = 5790825 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,683,979 reads read : 4,683,979 reads written : 4,683,979 spots read : 4,454,656 reads read : 4,454,656 reads written : 4,454,656 spots read : 4,441,594 reads read : 4,441,594 reads written : 4,441,594 2020-04-21T22:53:33 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 : 4,263,379 reads read : 4,263,379 reads written : 4,263,379 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: 00:02:46 17843608 reads; of these: 17843608 (100.00%) were unpaired; of these: 384532 (2.16%) aligned 0 times 15037822 (84.28%) aligned exactly 1 time 2421254 (13.57%) aligned >1 times 97.84% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 16994589 / 17459076 = 0.9734 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 08:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.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 08:01:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:01:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:01:33: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:01:33: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:01:33: #1 total tags in treatment: 464487 INFO @ Wed, 22 Apr 2020 08:01:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:33: #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 08:01:33: #1 tags after filtering in treatment: 464487 INFO @ Wed, 22 Apr 2020 08:01:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:01:33: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:33: #2 number of paired peaks: 446 WARNING @ Wed, 22 Apr 2020 08:01:33: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Wed, 22 Apr 2020 08:01:33: start model_add_line... INFO @ Wed, 22 Apr 2020 08:01:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:01:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:01:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:01:33: #2 predicted fragment length is 67 bps INFO @ Wed, 22 Apr 2020 08:01:33: #2 alternative fragment length(s) may be 4,44,67,136,162,176,206,228,257,284,309,411 bps INFO @ Wed, 22 Apr 2020 08:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.05_model.r WARNING @ Wed, 22 Apr 2020 08:01:33: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:01:33: #2 You may need to consider one of the other alternative d(s): 4,44,67,136,162,176,206,228,257,284,309,411 WARNING @ Wed, 22 Apr 2020 08:01:33: #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 08:01:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:01:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.05_summits.bed INFO @ Wed, 22 Apr 2020 08:01:34: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.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 08:01:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:01:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:02:02: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:02:02: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:02:02: #1 total tags in treatment: 464487 INFO @ Wed, 22 Apr 2020 08:02:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:02:02: #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 08:02:02: #1 tags after filtering in treatment: 464487 INFO @ Wed, 22 Apr 2020 08:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:02:02: #1 finished! INFO @ Wed, 22 Apr 2020 08:02:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:02:02: #2 number of paired peaks: 446 WARNING @ Wed, 22 Apr 2020 08:02:02: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Wed, 22 Apr 2020 08:02:02: start model_add_line... INFO @ Wed, 22 Apr 2020 08:02:02: start X-correlation... INFO @ Wed, 22 Apr 2020 08:02:02: end of X-cor INFO @ Wed, 22 Apr 2020 08:02:02: #2 finished! INFO @ Wed, 22 Apr 2020 08:02:02: #2 predicted fragment length is 67 bps INFO @ Wed, 22 Apr 2020 08:02:02: #2 alternative fragment length(s) may be 4,44,67,136,162,176,206,228,257,284,309,411 bps INFO @ Wed, 22 Apr 2020 08:02:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.10_model.r WARNING @ Wed, 22 Apr 2020 08:02:02: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:02:02: #2 You may need to consider one of the other alternative d(s): 4,44,67,136,162,176,206,228,257,284,309,411 WARNING @ Wed, 22 Apr 2020 08:02:02: #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 08:02:02: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:02:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.10_summits.bed INFO @ Wed, 22 Apr 2020 08:02:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:02:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.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 08:02:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:02:29: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:02:33: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:02:33: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:02:33: #1 total tags in treatment: 464487 INFO @ Wed, 22 Apr 2020 08:02:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:02:33: #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 08:02:33: #1 tags after filtering in treatment: 464487 INFO @ Wed, 22 Apr 2020 08:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:02:33: #1 finished! INFO @ Wed, 22 Apr 2020 08:02:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:02:33: #2 number of paired peaks: 446 WARNING @ Wed, 22 Apr 2020 08:02:33: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Wed, 22 Apr 2020 08:02:33: start model_add_line... INFO @ Wed, 22 Apr 2020 08:02:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:02:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:02:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:02:33: #2 predicted fragment length is 67 bps INFO @ Wed, 22 Apr 2020 08:02:33: #2 alternative fragment length(s) may be 4,44,67,136,162,176,206,228,257,284,309,411 bps INFO @ Wed, 22 Apr 2020 08:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.20_model.r WARNING @ Wed, 22 Apr 2020 08:02:33: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:02:33: #2 You may need to consider one of the other alternative d(s): 4,44,67,136,162,176,206,228,257,284,309,411 WARNING @ Wed, 22 Apr 2020 08:02:33: #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 08:02:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:02:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:02:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858302/ERX2858302.20_summits.bed INFO @ Wed, 22 Apr 2020 08:02:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling