Job ID = 14157870 SRX = SRX6799188 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36477308 spots for SRR10065395/SRR10065395.sra Written 36477308 spots for SRR10065395/SRR10065395.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158044 ("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: 00:08:46 36477308 reads; of these: 36477308 (100.00%) were unpaired; of these: 565013 (1.55%) aligned 0 times 25323624 (69.42%) aligned exactly 1 time 10588671 (29.03%) aligned >1 times 98.45% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:47 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] 11965674 / 35912295 = 0.3332 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 12:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.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 12:06:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:06:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:06:36: 1000000 INFO @ Wed, 08 Dec 2021 12:06:42: 2000000 INFO @ Wed, 08 Dec 2021 12:06:47: 3000000 INFO @ Wed, 08 Dec 2021 12:06:53: 4000000 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 12:06:59: 5000000 INFO @ Wed, 08 Dec 2021 12:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.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 12:07:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:07:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:07:05: 6000000 INFO @ Wed, 08 Dec 2021 12:07:06: 1000000 INFO @ Wed, 08 Dec 2021 12:07:11: 2000000 INFO @ Wed, 08 Dec 2021 12:07:12: 7000000 INFO @ Wed, 08 Dec 2021 12:07:17: 3000000 INFO @ Wed, 08 Dec 2021 12:07:18: 8000000 INFO @ Wed, 08 Dec 2021 12:07:23: 4000000 INFO @ Wed, 08 Dec 2021 12:07:23: 9000000 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 12:07:29: 10000000 INFO @ Wed, 08 Dec 2021 12:07:29: 5000000 INFO @ Wed, 08 Dec 2021 12:07:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.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 12:07:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:07:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:07:35: 11000000 INFO @ Wed, 08 Dec 2021 12:07:36: 6000000 INFO @ Wed, 08 Dec 2021 12:07:36: 1000000 INFO @ Wed, 08 Dec 2021 12:07:41: 12000000 INFO @ Wed, 08 Dec 2021 12:07:42: 2000000 INFO @ Wed, 08 Dec 2021 12:07:42: 7000000 INFO @ Wed, 08 Dec 2021 12:07:47: 13000000 INFO @ Wed, 08 Dec 2021 12:07:48: 3000000 INFO @ Wed, 08 Dec 2021 12:07:48: 8000000 INFO @ Wed, 08 Dec 2021 12:07:54: 14000000 INFO @ Wed, 08 Dec 2021 12:07:54: 4000000 INFO @ Wed, 08 Dec 2021 12:07:54: 9000000 INFO @ Wed, 08 Dec 2021 12:08:00: 10000000 INFO @ Wed, 08 Dec 2021 12:08:00: 15000000 INFO @ Wed, 08 Dec 2021 12:08:01: 5000000 INFO @ Wed, 08 Dec 2021 12:08:06: 11000000 INFO @ Wed, 08 Dec 2021 12:08:07: 6000000 INFO @ Wed, 08 Dec 2021 12:08:07: 16000000 INFO @ Wed, 08 Dec 2021 12:08:13: 12000000 INFO @ Wed, 08 Dec 2021 12:08:13: 7000000 INFO @ Wed, 08 Dec 2021 12:08:14: 17000000 INFO @ Wed, 08 Dec 2021 12:08:19: 13000000 INFO @ Wed, 08 Dec 2021 12:08:20: 8000000 INFO @ Wed, 08 Dec 2021 12:08:20: 18000000 INFO @ Wed, 08 Dec 2021 12:08:25: 14000000 INFO @ Wed, 08 Dec 2021 12:08:26: 9000000 INFO @ Wed, 08 Dec 2021 12:08:27: 19000000 INFO @ Wed, 08 Dec 2021 12:08:31: 10000000 INFO @ Wed, 08 Dec 2021 12:08:32: 15000000 INFO @ Wed, 08 Dec 2021 12:08:33: 20000000 INFO @ Wed, 08 Dec 2021 12:08:37: 11000000 INFO @ Wed, 08 Dec 2021 12:08:38: 16000000 INFO @ Wed, 08 Dec 2021 12:08:40: 21000000 INFO @ Wed, 08 Dec 2021 12:08:43: 12000000 INFO @ Wed, 08 Dec 2021 12:08:45: 17000000 INFO @ Wed, 08 Dec 2021 12:08:46: 22000000 INFO @ Wed, 08 Dec 2021 12:08:49: 13000000 INFO @ Wed, 08 Dec 2021 12:08:51: 18000000 INFO @ Wed, 08 Dec 2021 12:08:53: 23000000 INFO @ Wed, 08 Dec 2021 12:08:55: 14000000 INFO @ Wed, 08 Dec 2021 12:08:58: 19000000 INFO @ Wed, 08 Dec 2021 12:08:59: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:08:59: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:08:59: #1 total tags in treatment: 23946621 INFO @ Wed, 08 Dec 2021 12:08:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:08:59: #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 12:09:00: #1 tags after filtering in treatment: 23946621 INFO @ Wed, 08 Dec 2021 12:09:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:09:00: #1 finished! INFO @ Wed, 08 Dec 2021 12:09:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:09:01: #2 number of paired peaks: 385 WARNING @ Wed, 08 Dec 2021 12:09:01: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Wed, 08 Dec 2021 12:09:01: start model_add_line... INFO @ Wed, 08 Dec 2021 12:09:01: start X-correlation... INFO @ Wed, 08 Dec 2021 12:09:01: end of X-cor INFO @ Wed, 08 Dec 2021 12:09:01: #2 finished! INFO @ Wed, 08 Dec 2021 12:09:01: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:09:01: #2 alternative fragment length(s) may be 1 bps INFO @ Wed, 08 Dec 2021 12:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_model.r WARNING @ Wed, 08 Dec 2021 12:09:01: #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 12:09:01: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Wed, 08 Dec 2021 12:09:01: #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 12:09:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:09:02: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:09:04: 20000000 INFO @ Wed, 08 Dec 2021 12:09:08: 16000000 INFO @ Wed, 08 Dec 2021 12:09:11: 21000000 INFO @ Wed, 08 Dec 2021 12:09:15: 17000000 INFO @ Wed, 08 Dec 2021 12:09:17: 22000000 INFO @ Wed, 08 Dec 2021 12:09:21: 18000000 INFO @ Wed, 08 Dec 2021 12:09:24: 23000000 INFO @ Wed, 08 Dec 2021 12:09:28: 19000000 INFO @ Wed, 08 Dec 2021 12:09:30: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:09:30: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:09:30: #1 total tags in treatment: 23946621 INFO @ Wed, 08 Dec 2021 12:09:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:09:30: #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 12:09:30: #1 tags after filtering in treatment: 23946621 INFO @ Wed, 08 Dec 2021 12:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:09:30: #1 finished! INFO @ Wed, 08 Dec 2021 12:09:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:09:32: #2 number of paired peaks: 385 WARNING @ Wed, 08 Dec 2021 12:09:32: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Wed, 08 Dec 2021 12:09:32: start model_add_line... INFO @ Wed, 08 Dec 2021 12:09:32: start X-correlation... INFO @ Wed, 08 Dec 2021 12:09:32: end of X-cor INFO @ Wed, 08 Dec 2021 12:09:32: #2 finished! INFO @ Wed, 08 Dec 2021 12:09:32: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:09:32: #2 alternative fragment length(s) may be 1 bps INFO @ Wed, 08 Dec 2021 12:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_model.r WARNING @ Wed, 08 Dec 2021 12:09:32: #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 12:09:32: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Wed, 08 Dec 2021 12:09:32: #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 12:09:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:09:34: 20000000 INFO @ Wed, 08 Dec 2021 12:09:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:09:39: 21000000 INFO @ Wed, 08 Dec 2021 12:09:45: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_summits.bed INFO @ Wed, 08 Dec 2021 12:09:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:09:51: 23000000 INFO @ Wed, 08 Dec 2021 12:09:56: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:09:56: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:09:56: #1 total tags in treatment: 23946621 INFO @ Wed, 08 Dec 2021 12:09:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:09:56: #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 12:09:57: #1 tags after filtering in treatment: 23946621 INFO @ Wed, 08 Dec 2021 12:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:09:57: #1 finished! INFO @ Wed, 08 Dec 2021 12:09:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:09:58: #2 number of paired peaks: 385 WARNING @ Wed, 08 Dec 2021 12:09:58: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Wed, 08 Dec 2021 12:09:58: start model_add_line... INFO @ Wed, 08 Dec 2021 12:09:58: start X-correlation... INFO @ Wed, 08 Dec 2021 12:09:58: end of X-cor INFO @ Wed, 08 Dec 2021 12:09:58: #2 finished! INFO @ Wed, 08 Dec 2021 12:09:58: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:09:58: #2 alternative fragment length(s) may be 1 bps INFO @ Wed, 08 Dec 2021 12:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_model.r WARNING @ Wed, 08 Dec 2021 12:09:58: #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 12:09:58: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Wed, 08 Dec 2021 12:09:58: #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 12:09:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:10:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_summits.bed INFO @ Wed, 08 Dec 2021 12:10:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:10:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_summits.bed INFO @ Wed, 08 Dec 2021 12:10:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling