Job ID = 14159108 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 14159374 ("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: 00:08:54 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: 00:08:54 Overall time: 00:08:54 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:55:31: # 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 @ Wed, 08 Dec 2021 19:55:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:55:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:55:40: 1000000 INFO @ Wed, 08 Dec 2021 19:55:49: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:55:58: 3000000 INFO @ Wed, 08 Dec 2021 19:56:01: # 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 @ Wed, 08 Dec 2021 19:56:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:56:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:56:07: 4000000 INFO @ Wed, 08 Dec 2021 19:56:10: 1000000 INFO @ Wed, 08 Dec 2021 19:56:16: 5000000 INFO @ Wed, 08 Dec 2021 19:56:19: 2000000 INFO @ Wed, 08 Dec 2021 19:56:26: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:56:28: 3000000 INFO @ Wed, 08 Dec 2021 19:56:31: # 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 @ Wed, 08 Dec 2021 19:56:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:56:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:56:35: 7000000 INFO @ Wed, 08 Dec 2021 19:56:37: 4000000 INFO @ Wed, 08 Dec 2021 19:56:41: 1000000 INFO @ Wed, 08 Dec 2021 19:56:45: 8000000 INFO @ Wed, 08 Dec 2021 19:56:46: 5000000 INFO @ Wed, 08 Dec 2021 19:56:52: 2000000 INFO @ Wed, 08 Dec 2021 19:56:55: 6000000 INFO @ Wed, 08 Dec 2021 19:56:55: 9000000 INFO @ Wed, 08 Dec 2021 19:57:02: 3000000 INFO @ Wed, 08 Dec 2021 19:57:04: 7000000 INFO @ Wed, 08 Dec 2021 19:57:05: 10000000 INFO @ Wed, 08 Dec 2021 19:57:12: 4000000 INFO @ Wed, 08 Dec 2021 19:57:12: 8000000 INFO @ Wed, 08 Dec 2021 19:57:15: 11000000 INFO @ Wed, 08 Dec 2021 19:57:21: 9000000 INFO @ Wed, 08 Dec 2021 19:57:22: 5000000 INFO @ Wed, 08 Dec 2021 19:57:26: 12000000 INFO @ Wed, 08 Dec 2021 19:57:30: 10000000 INFO @ Wed, 08 Dec 2021 19:57:32: 6000000 INFO @ Wed, 08 Dec 2021 19:57:36: 13000000 INFO @ Wed, 08 Dec 2021 19:57:39: 11000000 INFO @ Wed, 08 Dec 2021 19:57:42: 7000000 INFO @ Wed, 08 Dec 2021 19:57:46: 14000000 INFO @ Wed, 08 Dec 2021 19:57:49: 12000000 INFO @ Wed, 08 Dec 2021 19:57:52: 8000000 INFO @ Wed, 08 Dec 2021 19:57:56: 15000000 INFO @ Wed, 08 Dec 2021 19:57:58: 13000000 INFO @ Wed, 08 Dec 2021 19:58:02: 9000000 INFO @ Wed, 08 Dec 2021 19:58:05: 16000000 INFO @ Wed, 08 Dec 2021 19:58:06: 14000000 INFO @ Wed, 08 Dec 2021 19:58:11: 10000000 INFO @ Wed, 08 Dec 2021 19:58:15: 15000000 INFO @ Wed, 08 Dec 2021 19:58:15: 17000000 INFO @ Wed, 08 Dec 2021 19:58:22: 11000000 INFO @ Wed, 08 Dec 2021 19:58:24: 16000000 INFO @ Wed, 08 Dec 2021 19:58:25: 18000000 INFO @ Wed, 08 Dec 2021 19:58:32: 12000000 INFO @ Wed, 08 Dec 2021 19:58:33: 17000000 INFO @ Wed, 08 Dec 2021 19:58:35: 19000000 INFO @ Wed, 08 Dec 2021 19:58:42: 18000000 INFO @ Wed, 08 Dec 2021 19:58:43: 13000000 INFO @ Wed, 08 Dec 2021 19:58:46: 20000000 INFO @ Wed, 08 Dec 2021 19:58:51: 19000000 INFO @ Wed, 08 Dec 2021 19:58:53: 14000000 INFO @ Wed, 08 Dec 2021 19:58:55: 21000000 INFO @ Wed, 08 Dec 2021 19:58:59: 20000000 INFO @ Wed, 08 Dec 2021 19:59:03: 15000000 INFO @ Wed, 08 Dec 2021 19:59:05: 22000000 INFO @ Wed, 08 Dec 2021 19:59:08: 21000000 INFO @ Wed, 08 Dec 2021 19:59:12: 16000000 INFO @ Wed, 08 Dec 2021 19:59:15: 23000000 INFO @ Wed, 08 Dec 2021 19:59:17: 22000000 INFO @ Wed, 08 Dec 2021 19:59:22: 17000000 INFO @ Wed, 08 Dec 2021 19:59:27: 24000000 INFO @ Wed, 08 Dec 2021 19:59:27: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:59:38: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 19:59:38: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 19:59:38: #1 total tags in treatment: 24860699 INFO @ Wed, 08 Dec 2021 19:59:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:59:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:59:38: #1 tags after filtering in treatment: 24860699 INFO @ Wed, 08 Dec 2021 19:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 19:59:38: #1 finished! INFO @ Wed, 08 Dec 2021 19:59:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:59:39: 24000000 INFO @ Wed, 08 Dec 2021 19:59:39: 18000000 INFO @ Wed, 08 Dec 2021 19:59:42: #2 number of paired peaks: 177 WARNING @ Wed, 08 Dec 2021 19:59:42: 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 @ Wed, 08 Dec 2021 19:59:42: start model_add_line... INFO @ Wed, 08 Dec 2021 19:59:42: start X-correlation... INFO @ Wed, 08 Dec 2021 19:59:42: end of X-cor INFO @ Wed, 08 Dec 2021 19:59:42: #2 finished! INFO @ Wed, 08 Dec 2021 19:59:42: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 19:59:42: #2 alternative fragment length(s) may be 1,19,47,493,526,567 bps INFO @ Wed, 08 Dec 2021 19:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_model.r WARNING @ Wed, 08 Dec 2021 19:59:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:59:42: #2 You may need to consider one of the other alternative d(s): 1,19,47,493,526,567 WARNING @ Wed, 08 Dec 2021 19:59:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 19:59:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:59:49: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 19:59:49: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 19:59:49: #1 total tags in treatment: 24860699 INFO @ Wed, 08 Dec 2021 19:59:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:59:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:59:50: #1 tags after filtering in treatment: 24860699 INFO @ Wed, 08 Dec 2021 19:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 19:59:50: #1 finished! INFO @ Wed, 08 Dec 2021 19:59:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:59:51: 19000000 INFO @ Wed, 08 Dec 2021 19:59:53: #2 number of paired peaks: 177 WARNING @ Wed, 08 Dec 2021 19:59:53: 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 @ Wed, 08 Dec 2021 19:59:53: start model_add_line... INFO @ Wed, 08 Dec 2021 19:59:54: start X-correlation... INFO @ Wed, 08 Dec 2021 19:59:54: end of X-cor INFO @ Wed, 08 Dec 2021 19:59:54: #2 finished! INFO @ Wed, 08 Dec 2021 19:59:54: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 19:59:54: #2 alternative fragment length(s) may be 1,19,47,493,526,567 bps INFO @ Wed, 08 Dec 2021 19:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_model.r WARNING @ Wed, 08 Dec 2021 19:59:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:59:54: #2 You may need to consider one of the other alternative d(s): 1,19,47,493,526,567 WARNING @ Wed, 08 Dec 2021 19:59:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 19:59:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:00:01: 20000000 INFO @ Wed, 08 Dec 2021 20:00:13: 21000000 INFO @ Wed, 08 Dec 2021 20:00:22: 22000000 INFO @ Wed, 08 Dec 2021 20:00:30: 23000000 INFO @ Wed, 08 Dec 2021 20:00:39: 24000000 INFO @ Wed, 08 Dec 2021 20:00:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:00:47: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:00:47: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:00:47: #1 total tags in treatment: 24860699 INFO @ Wed, 08 Dec 2021 20:00:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:00:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:00:48: #1 tags after filtering in treatment: 24860699 INFO @ Wed, 08 Dec 2021 20:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:00:48: #1 finished! INFO @ Wed, 08 Dec 2021 20:00:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:00:50: #2 number of paired peaks: 177 WARNING @ Wed, 08 Dec 2021 20:00:50: 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 @ Wed, 08 Dec 2021 20:00:50: start model_add_line... INFO @ Wed, 08 Dec 2021 20:00:50: start X-correlation... INFO @ Wed, 08 Dec 2021 20:00:50: end of X-cor INFO @ Wed, 08 Dec 2021 20:00:50: #2 finished! INFO @ Wed, 08 Dec 2021 20:00:50: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:00:50: #2 alternative fragment length(s) may be 1,19,47,493,526,567 bps INFO @ Wed, 08 Dec 2021 20:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_model.r WARNING @ Wed, 08 Dec 2021 20:00:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:00:50: #2 You may need to consider one of the other alternative d(s): 1,19,47,493,526,567 WARNING @ Wed, 08 Dec 2021 20:00:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:00:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:00:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:01:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.05_summits.bed INFO @ Wed, 08 Dec 2021 20:01:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.10_summits.bed INFO @ Wed, 08 Dec 2021 20:01:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:01:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120609/SRX9120609.20_summits.bed INFO @ Wed, 08 Dec 2021 20:02:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling