Job ID = 6366942 SRX = SRX2576643 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:01 prefetch.2.10.7: 1) Downloading 'SRR5272600'... 2020-06-15T23:20:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:38 prefetch.2.10.7: 1) 'SRR5272600' was downloaded successfully Read 18630839 spots for SRR5272600/SRR5272600.sra Written 18630839 spots for SRR5272600/SRR5272600.sra 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: 00:04:34 18630839 reads; of these: 18630839 (100.00%) were unpaired; of these: 415738 (2.23%) aligned 0 times 14985707 (80.43%) aligned exactly 1 time 3229394 (17.33%) aligned >1 times 97.77% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3412035 / 18215101 = 0.1873 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 @ Tue, 16 Jun 2020 08:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:32:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:24: 1000000 INFO @ Tue, 16 Jun 2020 08:32:30: 2000000 INFO @ Tue, 16 Jun 2020 08:32:37: 3000000 INFO @ Tue, 16 Jun 2020 08:32:44: 4000000 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 @ Tue, 16 Jun 2020 08:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:32:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:50: 5000000 INFO @ Tue, 16 Jun 2020 08:32:54: 1000000 INFO @ Tue, 16 Jun 2020 08:32:57: 6000000 INFO @ Tue, 16 Jun 2020 08:33:00: 2000000 INFO @ Tue, 16 Jun 2020 08:33:04: 7000000 INFO @ Tue, 16 Jun 2020 08:33:06: 3000000 INFO @ Tue, 16 Jun 2020 08:33:11: 8000000 INFO @ Tue, 16 Jun 2020 08:33:12: 4000000 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 @ Tue, 16 Jun 2020 08:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:33:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:18: 9000000 INFO @ Tue, 16 Jun 2020 08:33:18: 5000000 INFO @ Tue, 16 Jun 2020 08:33:24: 1000000 INFO @ Tue, 16 Jun 2020 08:33:25: 6000000 INFO @ Tue, 16 Jun 2020 08:33:25: 10000000 INFO @ Tue, 16 Jun 2020 08:33:31: 7000000 INFO @ Tue, 16 Jun 2020 08:33:31: 2000000 INFO @ Tue, 16 Jun 2020 08:33:32: 11000000 INFO @ Tue, 16 Jun 2020 08:33:37: 8000000 INFO @ Tue, 16 Jun 2020 08:33:39: 3000000 INFO @ Tue, 16 Jun 2020 08:33:39: 12000000 INFO @ Tue, 16 Jun 2020 08:33:44: 9000000 INFO @ Tue, 16 Jun 2020 08:33:46: 4000000 INFO @ Tue, 16 Jun 2020 08:33:46: 13000000 INFO @ Tue, 16 Jun 2020 08:33:50: 10000000 INFO @ Tue, 16 Jun 2020 08:33:53: 5000000 INFO @ Tue, 16 Jun 2020 08:33:53: 14000000 INFO @ Tue, 16 Jun 2020 08:33:56: 11000000 INFO @ Tue, 16 Jun 2020 08:33:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:59: #1 total tags in treatment: 14803066 INFO @ Tue, 16 Jun 2020 08:33:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:33:59: #1 tags after filtering in treatment: 14803066 INFO @ Tue, 16 Jun 2020 08:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:00: 6000000 INFO @ Tue, 16 Jun 2020 08:34:00: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 08:34:00: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:01: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:34:01: #2 alternative fragment length(s) may be 2,49,561 bps INFO @ Tue, 16 Jun 2020 08:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:01: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:01: #2 You may need to consider one of the other alternative d(s): 2,49,561 WARNING @ Tue, 16 Jun 2020 08:34:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:34:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:02: 12000000 INFO @ Tue, 16 Jun 2020 08:34:07: 7000000 INFO @ Tue, 16 Jun 2020 08:34:09: 13000000 INFO @ Tue, 16 Jun 2020 08:34:15: 14000000 INFO @ Tue, 16 Jun 2020 08:34:15: 8000000 INFO @ Tue, 16 Jun 2020 08:34:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:20: #1 total tags in treatment: 14803066 INFO @ Tue, 16 Jun 2020 08:34:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:34:20: #1 tags after filtering in treatment: 14803066 INFO @ Tue, 16 Jun 2020 08:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:21: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 08:34:21: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:21: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:34:21: #2 alternative fragment length(s) may be 2,49,561 bps INFO @ Tue, 16 Jun 2020 08:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.10_model.r WARNING @ Tue, 16 Jun 2020 08:34:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:21: #2 You may need to consider one of the other alternative d(s): 2,49,561 WARNING @ Tue, 16 Jun 2020 08:34:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:34:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:22: 9000000 INFO @ Tue, 16 Jun 2020 08:34:30: 10000000 INFO @ Tue, 16 Jun 2020 08:34:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:37: 11000000 INFO @ Tue, 16 Jun 2020 08:34:43: 12000000 INFO @ Tue, 16 Jun 2020 08:34:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1226 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:50: 13000000 INFO @ Tue, 16 Jun 2020 08:34:57: 14000000 INFO @ Tue, 16 Jun 2020 08:35:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:35:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:35:03: #1 total tags in treatment: 14803066 INFO @ Tue, 16 Jun 2020 08:35:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:35:03: #1 tags after filtering in treatment: 14803066 INFO @ Tue, 16 Jun 2020 08:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:04: Done! INFO @ Tue, 16 Jun 2020 08:35:04: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 08:35:04: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:04: start model_add_line... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (730 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:04: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:35:04: #2 alternative fragment length(s) may be 2,49,561 bps INFO @ Tue, 16 Jun 2020 08:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:04: #2 You may need to consider one of the other alternative d(s): 2,49,561 WARNING @ Tue, 16 Jun 2020 08:35:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:35:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576643/SRX2576643.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (249 records, 4 fields): 2 millis CompletedMACS2peakCalling