Job ID = 14157872 SRX = SRX6799190 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34174635 spots for SRR10065397/SRR10065397.sra Written 34174635 spots for SRR10065397/SRR10065397.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158051 ("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: 00:08:09 34174635 reads; of these: 34174635 (100.00%) were unpaired; of these: 1373911 (4.02%) aligned 0 times 22951237 (67.16%) aligned exactly 1 time 9849487 (28.82%) aligned >1 times 95.98% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 10050366 / 32800724 = 0.3064 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 12:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.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 12:08:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:08:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:08:19: 1000000 INFO @ Wed, 08 Dec 2021 12:08:23: 2000000 INFO @ Wed, 08 Dec 2021 12:08:28: 3000000 INFO @ Wed, 08 Dec 2021 12:08:32: 4000000 INFO @ Wed, 08 Dec 2021 12:08:37: 5000000 INFO @ Wed, 08 Dec 2021 12:08:41: 6000000 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 12:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.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 12:08:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:08:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:08:46: 7000000 INFO @ Wed, 08 Dec 2021 12:08:49: 1000000 INFO @ Wed, 08 Dec 2021 12:08:50: 8000000 INFO @ Wed, 08 Dec 2021 12:08:53: 2000000 INFO @ Wed, 08 Dec 2021 12:08:55: 9000000 INFO @ Wed, 08 Dec 2021 12:08:58: 3000000 INFO @ Wed, 08 Dec 2021 12:08:59: 10000000 INFO @ Wed, 08 Dec 2021 12:09:02: 4000000 INFO @ Wed, 08 Dec 2021 12:09:04: 11000000 INFO @ Wed, 08 Dec 2021 12:09:07: 5000000 INFO @ Wed, 08 Dec 2021 12:09:09: 12000000 INFO @ Wed, 08 Dec 2021 12:09:12: 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 12:09:13: 13000000 INFO @ Wed, 08 Dec 2021 12:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.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 12:09:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:09:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:09:16: 7000000 INFO @ Wed, 08 Dec 2021 12:09:18: 14000000 INFO @ Wed, 08 Dec 2021 12:09:19: 1000000 INFO @ Wed, 08 Dec 2021 12:09:21: 8000000 INFO @ Wed, 08 Dec 2021 12:09:23: 15000000 INFO @ Wed, 08 Dec 2021 12:09:25: 2000000 INFO @ Wed, 08 Dec 2021 12:09:26: 9000000 INFO @ Wed, 08 Dec 2021 12:09:27: 16000000 INFO @ Wed, 08 Dec 2021 12:09:30: 10000000 INFO @ Wed, 08 Dec 2021 12:09:30: 3000000 INFO @ Wed, 08 Dec 2021 12:09:32: 17000000 INFO @ Wed, 08 Dec 2021 12:09:35: 11000000 INFO @ Wed, 08 Dec 2021 12:09:36: 4000000 INFO @ Wed, 08 Dec 2021 12:09:37: 18000000 INFO @ Wed, 08 Dec 2021 12:09:39: 12000000 INFO @ Wed, 08 Dec 2021 12:09:41: 5000000 INFO @ Wed, 08 Dec 2021 12:09:41: 19000000 INFO @ Wed, 08 Dec 2021 12:09:44: 13000000 INFO @ Wed, 08 Dec 2021 12:09:46: 20000000 INFO @ Wed, 08 Dec 2021 12:09:47: 6000000 INFO @ Wed, 08 Dec 2021 12:09:49: 14000000 INFO @ Wed, 08 Dec 2021 12:09:51: 21000000 INFO @ Wed, 08 Dec 2021 12:09:52: 7000000 INFO @ Wed, 08 Dec 2021 12:09:54: 15000000 INFO @ Wed, 08 Dec 2021 12:09:56: 22000000 INFO @ Wed, 08 Dec 2021 12:09:57: 8000000 INFO @ Wed, 08 Dec 2021 12:09:58: 16000000 INFO @ Wed, 08 Dec 2021 12:09:59: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 12:09:59: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 12:09:59: #1 total tags in treatment: 22750358 INFO @ Wed, 08 Dec 2021 12:09:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:09:59: #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 12:10:00: #1 tags after filtering in treatment: 22750358 INFO @ Wed, 08 Dec 2021 12:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:10:00: #1 finished! INFO @ Wed, 08 Dec 2021 12:10:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:10:01: #2 number of paired peaks: 405 WARNING @ Wed, 08 Dec 2021 12:10:01: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Wed, 08 Dec 2021 12:10:01: start model_add_line... INFO @ Wed, 08 Dec 2021 12:10:01: start X-correlation... INFO @ Wed, 08 Dec 2021 12:10:01: end of X-cor INFO @ Wed, 08 Dec 2021 12:10:01: #2 finished! INFO @ Wed, 08 Dec 2021 12:10:01: #2 predicted fragment length is 2 bps INFO @ Wed, 08 Dec 2021 12:10:01: #2 alternative fragment length(s) may be 2,19,37 bps INFO @ Wed, 08 Dec 2021 12:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_model.r WARNING @ Wed, 08 Dec 2021 12:10:01: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:10:01: #2 You may need to consider one of the other alternative d(s): 2,19,37 WARNING @ Wed, 08 Dec 2021 12:10:01: #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 12:10:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:10:03: 9000000 INFO @ Wed, 08 Dec 2021 12:10:03: 17000000 INFO @ Wed, 08 Dec 2021 12:10:08: 18000000 INFO @ Wed, 08 Dec 2021 12:10:08: 10000000 INFO @ Wed, 08 Dec 2021 12:10:13: 19000000 INFO @ Wed, 08 Dec 2021 12:10:13: 11000000 INFO @ Wed, 08 Dec 2021 12:10:17: 20000000 INFO @ Wed, 08 Dec 2021 12:10:18: 12000000 INFO @ Wed, 08 Dec 2021 12:10:22: 21000000 INFO @ Wed, 08 Dec 2021 12:10:24: 13000000 INFO @ Wed, 08 Dec 2021 12:10:27: 22000000 INFO @ Wed, 08 Dec 2021 12:10:29: 14000000 INFO @ Wed, 08 Dec 2021 12:10:30: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 12:10:30: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 12:10:30: #1 total tags in treatment: 22750358 INFO @ Wed, 08 Dec 2021 12:10:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:10:30: #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 12:10:31: #1 tags after filtering in treatment: 22750358 INFO @ Wed, 08 Dec 2021 12:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:10:31: #1 finished! INFO @ Wed, 08 Dec 2021 12:10:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:10:32: #2 number of paired peaks: 405 WARNING @ Wed, 08 Dec 2021 12:10:32: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Wed, 08 Dec 2021 12:10:32: start model_add_line... INFO @ Wed, 08 Dec 2021 12:10:32: start X-correlation... INFO @ Wed, 08 Dec 2021 12:10:32: end of X-cor INFO @ Wed, 08 Dec 2021 12:10:32: #2 finished! INFO @ Wed, 08 Dec 2021 12:10:32: #2 predicted fragment length is 2 bps INFO @ Wed, 08 Dec 2021 12:10:32: #2 alternative fragment length(s) may be 2,19,37 bps INFO @ Wed, 08 Dec 2021 12:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_model.r WARNING @ Wed, 08 Dec 2021 12:10:32: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:10:32: #2 You may need to consider one of the other alternative d(s): 2,19,37 WARNING @ Wed, 08 Dec 2021 12:10:32: #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 12:10:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:10:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:10:35: 15000000 INFO @ Wed, 08 Dec 2021 12:10:40: 16000000 INFO @ Wed, 08 Dec 2021 12:10:45: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_summits.bed INFO @ Wed, 08 Dec 2021 12:10:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:10:51: 18000000 INFO @ Wed, 08 Dec 2021 12:10:56: 19000000 INFO @ Wed, 08 Dec 2021 12:11:01: 20000000 INFO @ Wed, 08 Dec 2021 12:11:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:11:07: 21000000 INFO @ Wed, 08 Dec 2021 12:11:12: 22000000 INFO @ Wed, 08 Dec 2021 12:11:16: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 12:11:16: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 12:11:16: #1 total tags in treatment: 22750358 INFO @ Wed, 08 Dec 2021 12:11:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:11:16: #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 12:11:17: #1 tags after filtering in treatment: 22750358 INFO @ Wed, 08 Dec 2021 12:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:11:17: #1 finished! INFO @ Wed, 08 Dec 2021 12:11:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:11:18: #2 number of paired peaks: 405 WARNING @ Wed, 08 Dec 2021 12:11:18: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Wed, 08 Dec 2021 12:11:18: start model_add_line... INFO @ Wed, 08 Dec 2021 12:11:18: start X-correlation... INFO @ Wed, 08 Dec 2021 12:11:18: end of X-cor INFO @ Wed, 08 Dec 2021 12:11:18: #2 finished! INFO @ Wed, 08 Dec 2021 12:11:18: #2 predicted fragment length is 2 bps INFO @ Wed, 08 Dec 2021 12:11:18: #2 alternative fragment length(s) may be 2,19,37 bps INFO @ Wed, 08 Dec 2021 12:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_model.r WARNING @ Wed, 08 Dec 2021 12:11:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:11:18: #2 You may need to consider one of the other alternative d(s): 2,19,37 WARNING @ Wed, 08 Dec 2021 12:11:18: #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 12:11:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_summits.bed INFO @ Wed, 08 Dec 2021 12:11:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:11:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_summits.bed INFO @ Wed, 08 Dec 2021 12:12:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling