Job ID = 16432205 SRX = SRX15407769 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:31:55 prefetch.2.10.7: 1) Downloading 'SRR19348982'... 2022-08-02T00:31:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:32:17 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:32:17 prefetch.2.10.7: 'SRR19348982' is valid 2022-08-02T00:32:17 prefetch.2.10.7: 1) 'SRR19348982' was downloaded successfully 2022-08-02T00:32:17 prefetch.2.10.7: 'SRR19348982' has 0 unresolved dependencies Read 11193660 spots for SRR19348982/SRR19348982.sra Written 11193660 spots for SRR19348982/SRR19348982.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433165 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:00 11193660 reads; of these: 11193660 (100.00%) were unpaired; of these: 7725476 (69.02%) aligned 0 times 2974757 (26.58%) aligned exactly 1 time 493427 (4.41%) aligned >1 times 30.98% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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_rmdupse_core] 747458 / 3468184 = 0.2155 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.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, 02 Aug 2022 09:36:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:36:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:36:19: 1000000 INFO @ Tue, 02 Aug 2022 09:36:24: 2000000 INFO @ Tue, 02 Aug 2022 09:36:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:36:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:36:28: #1 total tags in treatment: 2720726 INFO @ Tue, 02 Aug 2022 09:36:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:36:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:36:28: #1 tags after filtering in treatment: 2720726 INFO @ Tue, 02 Aug 2022 09:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:36:28: #1 finished! INFO @ Tue, 02 Aug 2022 09:36:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:36:29: #2 number of paired peaks: 383 WARNING @ Tue, 02 Aug 2022 09:36:29: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Tue, 02 Aug 2022 09:36:29: start model_add_line... INFO @ Tue, 02 Aug 2022 09:36:29: start X-correlation... INFO @ Tue, 02 Aug 2022 09:36:29: end of X-cor INFO @ Tue, 02 Aug 2022 09:36:29: #2 finished! INFO @ Tue, 02 Aug 2022 09:36:29: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 09:36:29: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 09:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.05_model.r WARNING @ Tue, 02 Aug 2022 09:36:29: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:36:29: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 09:36:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:36:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:36:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:36:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.05_summits.bed INFO @ Tue, 02 Aug 2022 09:36:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (702 records, 4 fields): 48 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.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, 02 Aug 2022 09:36:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:36:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:36:48: 1000000 INFO @ Tue, 02 Aug 2022 09:36:54: 2000000 INFO @ Tue, 02 Aug 2022 09:36:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:36:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:36:58: #1 total tags in treatment: 2720726 INFO @ Tue, 02 Aug 2022 09:36:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:36:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:36:58: #1 tags after filtering in treatment: 2720726 INFO @ Tue, 02 Aug 2022 09:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:36:58: #1 finished! INFO @ Tue, 02 Aug 2022 09:36:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:36:58: #2 number of paired peaks: 383 WARNING @ Tue, 02 Aug 2022 09:36:58: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Tue, 02 Aug 2022 09:36:58: start model_add_line... INFO @ Tue, 02 Aug 2022 09:36:58: start X-correlation... INFO @ Tue, 02 Aug 2022 09:36:58: end of X-cor INFO @ Tue, 02 Aug 2022 09:36:58: #2 finished! INFO @ Tue, 02 Aug 2022 09:36:58: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 09:36:58: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 09:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.10_model.r WARNING @ Tue, 02 Aug 2022 09:36:58: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:36:58: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 09:36:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:36:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:37:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:37:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:37:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:37:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.10_summits.bed INFO @ Tue, 02 Aug 2022 09:37:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.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, 02 Aug 2022 09:37:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:37:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:37:18: 1000000 INFO @ Tue, 02 Aug 2022 09:37:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:37:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:37:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:37:27: #1 total tags in treatment: 2720726 INFO @ Tue, 02 Aug 2022 09:37:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:37:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:37:27: #1 tags after filtering in treatment: 2720726 INFO @ Tue, 02 Aug 2022 09:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:37:27: #1 finished! INFO @ Tue, 02 Aug 2022 09:37:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:37:28: #2 number of paired peaks: 383 WARNING @ Tue, 02 Aug 2022 09:37:28: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Tue, 02 Aug 2022 09:37:28: start model_add_line... INFO @ Tue, 02 Aug 2022 09:37:28: start X-correlation... INFO @ Tue, 02 Aug 2022 09:37:28: end of X-cor INFO @ Tue, 02 Aug 2022 09:37:28: #2 finished! INFO @ Tue, 02 Aug 2022 09:37:28: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 09:37:28: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 09:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.20_model.r WARNING @ Tue, 02 Aug 2022 09:37:28: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:37:28: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 09:37:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:37:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:37:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:37:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:37:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:37:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:37:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407769/SRX15407769.20_summits.bed INFO @ Tue, 02 Aug 2022 09:37:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 35 millis CompletedMACS2peakCalling