Job ID = 10165773 SRX = SRX9120609 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 40312738 spots for SRR12638552/SRR12638552.sra Written 40312738 spots for SRR12638552/SRR12638552.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166116 ("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: 00:07:55 40312738 reads; of these: 40312738 (100.00%) were unpaired; of these: 9411228 (23.35%) aligned 0 times 25579925 (63.45%) aligned exactly 1 time 5321585 (13.20%) aligned >1 times 76.65% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6040811 / 30901510 = 0.1955 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 @ Thu, 08 Oct 2020 20:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.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 @ Thu, 08 Oct 2020 20:07:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:07:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:02: 1000000 INFO @ Thu, 08 Oct 2020 20:08:07: 2000000 INFO @ Thu, 08 Oct 2020 20:08:13: 3000000 INFO @ Thu, 08 Oct 2020 20:08:18: 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 @ Thu, 08 Oct 2020 20:08:23: 5000000 INFO @ Thu, 08 Oct 2020 20:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.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 @ Thu, 08 Oct 2020 20:08:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:08:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:29: 6000000 INFO @ Thu, 08 Oct 2020 20:08:30: 1000000 INFO @ Thu, 08 Oct 2020 20:08:35: 7000000 INFO @ Thu, 08 Oct 2020 20:08:36: 2000000 INFO @ Thu, 08 Oct 2020 20:08:41: 8000000 INFO @ Thu, 08 Oct 2020 20:08:42: 3000000 INFO @ Thu, 08 Oct 2020 20:08:46: 9000000 INFO @ Thu, 08 Oct 2020 20:08:48: 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 @ Thu, 08 Oct 2020 20:08:52: 10000000 INFO @ Thu, 08 Oct 2020 20:08:54: 5000000 INFO @ Thu, 08 Oct 2020 20:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.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 @ Thu, 08 Oct 2020 20:08:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:08:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:59: 11000000 INFO @ Thu, 08 Oct 2020 20:09:00: 6000000 INFO @ Thu, 08 Oct 2020 20:09:00: 1000000 INFO @ Thu, 08 Oct 2020 20:09:05: 12000000 INFO @ Thu, 08 Oct 2020 20:09:07: 7000000 INFO @ Thu, 08 Oct 2020 20:09:07: 2000000 INFO @ Thu, 08 Oct 2020 20:09:12: 13000000 INFO @ Thu, 08 Oct 2020 20:09:14: 8000000 INFO @ Thu, 08 Oct 2020 20:09:14: 3000000 INFO @ Thu, 08 Oct 2020 20:09:19: 14000000 INFO @ Thu, 08 Oct 2020 20:09:20: 9000000 INFO @ Thu, 08 Oct 2020 20:09:21: 4000000 INFO @ Thu, 08 Oct 2020 20:09:26: 15000000 INFO @ Thu, 08 Oct 2020 20:09:27: 5000000 INFO @ Thu, 08 Oct 2020 20:09:27: 10000000 INFO @ Thu, 08 Oct 2020 20:09:32: 16000000 INFO @ Thu, 08 Oct 2020 20:09:33: 6000000 INFO @ Thu, 08 Oct 2020 20:09:34: 11000000 INFO @ Thu, 08 Oct 2020 20:09:39: 17000000 INFO @ Thu, 08 Oct 2020 20:09:40: 7000000 INFO @ Thu, 08 Oct 2020 20:09:40: 12000000 INFO @ Thu, 08 Oct 2020 20:09:46: 18000000 INFO @ Thu, 08 Oct 2020 20:09:46: 8000000 INFO @ Thu, 08 Oct 2020 20:09:47: 13000000 INFO @ Thu, 08 Oct 2020 20:09:52: 9000000 INFO @ Thu, 08 Oct 2020 20:09:52: 19000000 INFO @ Thu, 08 Oct 2020 20:09:53: 14000000 INFO @ Thu, 08 Oct 2020 20:09:59: 10000000 INFO @ Thu, 08 Oct 2020 20:09:59: 20000000 INFO @ Thu, 08 Oct 2020 20:10:00: 15000000 INFO @ Thu, 08 Oct 2020 20:10:05: 11000000 INFO @ Thu, 08 Oct 2020 20:10:06: 21000000 INFO @ Thu, 08 Oct 2020 20:10:06: 16000000 INFO @ Thu, 08 Oct 2020 20:10:11: 12000000 INFO @ Thu, 08 Oct 2020 20:10:12: 22000000 INFO @ Thu, 08 Oct 2020 20:10:13: 17000000 INFO @ Thu, 08 Oct 2020 20:10:18: 13000000 INFO @ Thu, 08 Oct 2020 20:10:19: 18000000 INFO @ Thu, 08 Oct 2020 20:10:19: 23000000 INFO @ Thu, 08 Oct 2020 20:10:24: 14000000 INFO @ Thu, 08 Oct 2020 20:10:25: 19000000 INFO @ Thu, 08 Oct 2020 20:10:26: 24000000 INFO @ Thu, 08 Oct 2020 20:10:31: 15000000 INFO @ Thu, 08 Oct 2020 20:10:31: 20000000 INFO @ Thu, 08 Oct 2020 20:10:31: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:10:31: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:10:31: #1 total tags in treatment: 24860699 INFO @ Thu, 08 Oct 2020 20:10:31: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:10:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:10:32: #1 tags after filtering in treatment: 24860699 INFO @ Thu, 08 Oct 2020 20:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:10:32: #1 finished! INFO @ Thu, 08 Oct 2020 20:10:32: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:10:33: #2 number of paired peaks: 177 WARNING @ Thu, 08 Oct 2020 20:10:33: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Thu, 08 Oct 2020 20:10:33: start model_add_line... INFO @ Thu, 08 Oct 2020 20:10:34: start X-correlation... INFO @ Thu, 08 Oct 2020 20:10:34: end of X-cor INFO @ Thu, 08 Oct 2020 20:10:34: #2 finished! INFO @ Thu, 08 Oct 2020 20:10:34: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:10:34: #2 alternative fragment length(s) may be 1,19,47,493,526,567 bps INFO @ Thu, 08 Oct 2020 20:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_model.r WARNING @ Thu, 08 Oct 2020 20:10:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:10:34: #2 You may need to consider one of the other alternative d(s): 1,19,47,493,526,567 WARNING @ Thu, 08 Oct 2020 20:10:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:10:34: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:10:36: 16000000 INFO @ Thu, 08 Oct 2020 20:10:37: 21000000 INFO @ Thu, 08 Oct 2020 20:10:42: 17000000 INFO @ Thu, 08 Oct 2020 20:10:43: 22000000 INFO @ Thu, 08 Oct 2020 20:10:48: 18000000 INFO @ Thu, 08 Oct 2020 20:10:49: 23000000 INFO @ Thu, 08 Oct 2020 20:10:54: 19000000 INFO @ Thu, 08 Oct 2020 20:10:54: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:10:59: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:10:59: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:10:59: #1 total tags in treatment: 24860699 INFO @ Thu, 08 Oct 2020 20:10:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:10:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:11:00: 20000000 INFO @ Thu, 08 Oct 2020 20:11:00: #1 tags after filtering in treatment: 24860699 INFO @ Thu, 08 Oct 2020 20:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:11:00: #1 finished! INFO @ Thu, 08 Oct 2020 20:11:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:11:01: #2 number of paired peaks: 177 WARNING @ Thu, 08 Oct 2020 20:11:01: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Thu, 08 Oct 2020 20:11:01: start model_add_line... INFO @ Thu, 08 Oct 2020 20:11:02: start X-correlation... INFO @ Thu, 08 Oct 2020 20:11:02: end of X-cor INFO @ Thu, 08 Oct 2020 20:11:02: #2 finished! INFO @ Thu, 08 Oct 2020 20:11:02: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:11:02: #2 alternative fragment length(s) may be 1,19,47,493,526,567 bps INFO @ Thu, 08 Oct 2020 20:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_model.r WARNING @ Thu, 08 Oct 2020 20:11:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:11:02: #2 You may need to consider one of the other alternative d(s): 1,19,47,493,526,567 WARNING @ Thu, 08 Oct 2020 20:11:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:11:02: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:11:05: 21000000 INFO @ Thu, 08 Oct 2020 20:11:07: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:11:11: 22000000 INFO @ Thu, 08 Oct 2020 20:11:16: 23000000 INFO @ Thu, 08 Oct 2020 20:11:22: 24000000 INFO @ Thu, 08 Oct 2020 20:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_summits.bed INFO @ Thu, 08 Oct 2020 20:11:25: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:11:28: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:11:28: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:11:28: #1 total tags in treatment: 24860699 INFO @ Thu, 08 Oct 2020 20:11:28: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:11:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:11:28: #1 tags after filtering in treatment: 24860699 INFO @ Thu, 08 Oct 2020 20:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:11:28: #1 finished! INFO @ Thu, 08 Oct 2020 20:11:28: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:11:30: #2 number of paired peaks: 177 WARNING @ Thu, 08 Oct 2020 20:11:30: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Thu, 08 Oct 2020 20:11:30: start model_add_line... INFO @ Thu, 08 Oct 2020 20:11:30: start X-correlation... INFO @ Thu, 08 Oct 2020 20:11:30: end of X-cor INFO @ Thu, 08 Oct 2020 20:11:30: #2 finished! INFO @ Thu, 08 Oct 2020 20:11:30: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:11:30: #2 alternative fragment length(s) may be 1,19,47,493,526,567 bps INFO @ Thu, 08 Oct 2020 20:11:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_model.r WARNING @ Thu, 08 Oct 2020 20:11:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:11:30: #2 You may need to consider one of the other alternative d(s): 1,19,47,493,526,567 WARNING @ Thu, 08 Oct 2020 20:11:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:11:30: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:11:36: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:11:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:11:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:11:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_summits.bed INFO @ Thu, 08 Oct 2020 20:11:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:12:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_summits.bed INFO @ Thu, 08 Oct 2020 20:12:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling