Job ID = 14159374 SRX = SRX9120609 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:31 40312738 reads; of these: 40312738 (100.00%) were unpaired; of these: 9410576 (23.34%) aligned 0 times 25580423 (63.45%) aligned exactly 1 time 5321739 (13.20%) aligned >1 times 76.66% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 6041170 / 30902162 = 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 21:30:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:30:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:30:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:30:47: 1000000 INFO @ Wed, 08 Dec 2021 21:30:52: 2000000 INFO @ Wed, 08 Dec 2021 21:30:57: 3000000 INFO @ Wed, 08 Dec 2021 21:31:02: 4000000 INFO @ Wed, 08 Dec 2021 21:31:07: 5000000 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 21:31:12: 6000000 INFO @ Wed, 08 Dec 2021 21:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:31:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:31:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:31:18: 7000000 INFO @ Wed, 08 Dec 2021 21:31:18: 1000000 INFO @ Wed, 08 Dec 2021 21:31:23: 8000000 INFO @ Wed, 08 Dec 2021 21:31:24: 2000000 INFO @ Wed, 08 Dec 2021 21:31:29: 9000000 INFO @ Wed, 08 Dec 2021 21:31:29: 3000000 INFO @ Wed, 08 Dec 2021 21:31:35: 10000000 INFO @ Wed, 08 Dec 2021 21:31:35: 4000000 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 21:31:40: 11000000 INFO @ Wed, 08 Dec 2021 21:31:40: 5000000 INFO @ Wed, 08 Dec 2021 21:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:31:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:31:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:31:46: 6000000 INFO @ Wed, 08 Dec 2021 21:31:46: 12000000 INFO @ Wed, 08 Dec 2021 21:31:47: 1000000 INFO @ Wed, 08 Dec 2021 21:31:51: 7000000 INFO @ Wed, 08 Dec 2021 21:31:52: 13000000 INFO @ Wed, 08 Dec 2021 21:31:53: 2000000 INFO @ Wed, 08 Dec 2021 21:31:57: 8000000 INFO @ Wed, 08 Dec 2021 21:31:57: 14000000 INFO @ Wed, 08 Dec 2021 21:31:58: 3000000 INFO @ Wed, 08 Dec 2021 21:32:03: 9000000 INFO @ Wed, 08 Dec 2021 21:32:03: 15000000 INFO @ Wed, 08 Dec 2021 21:32:04: 4000000 INFO @ Wed, 08 Dec 2021 21:32:08: 10000000 INFO @ Wed, 08 Dec 2021 21:32:09: 16000000 INFO @ Wed, 08 Dec 2021 21:32:10: 5000000 INFO @ Wed, 08 Dec 2021 21:32:14: 11000000 INFO @ Wed, 08 Dec 2021 21:32:14: 17000000 INFO @ Wed, 08 Dec 2021 21:32:15: 6000000 INFO @ Wed, 08 Dec 2021 21:32:20: 12000000 INFO @ Wed, 08 Dec 2021 21:32:20: 18000000 INFO @ Wed, 08 Dec 2021 21:32:21: 7000000 INFO @ Wed, 08 Dec 2021 21:32:25: 13000000 INFO @ Wed, 08 Dec 2021 21:32:26: 19000000 INFO @ Wed, 08 Dec 2021 21:32:27: 8000000 INFO @ Wed, 08 Dec 2021 21:32:31: 14000000 INFO @ Wed, 08 Dec 2021 21:32:31: 20000000 INFO @ Wed, 08 Dec 2021 21:32:33: 9000000 INFO @ Wed, 08 Dec 2021 21:32:37: 15000000 INFO @ Wed, 08 Dec 2021 21:32:37: 21000000 INFO @ Wed, 08 Dec 2021 21:32:38: 10000000 INFO @ Wed, 08 Dec 2021 21:32:43: 16000000 INFO @ Wed, 08 Dec 2021 21:32:43: 22000000 INFO @ Wed, 08 Dec 2021 21:32:44: 11000000 INFO @ Wed, 08 Dec 2021 21:32:48: 17000000 INFO @ Wed, 08 Dec 2021 21:32:49: 23000000 INFO @ Wed, 08 Dec 2021 21:32:50: 12000000 INFO @ Wed, 08 Dec 2021 21:32:54: 18000000 INFO @ Wed, 08 Dec 2021 21:32:54: 24000000 INFO @ Wed, 08 Dec 2021 21:32:55: 13000000 INFO @ Wed, 08 Dec 2021 21:32:59: 19000000 INFO @ Wed, 08 Dec 2021 21:32:59: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:32:59: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:32:59: #1 total tags in treatment: 24860992 INFO @ Wed, 08 Dec 2021 21:32:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:32:59: #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 21:33:00: #1 tags after filtering in treatment: 24860992 INFO @ Wed, 08 Dec 2021 21:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:33:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:33:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:33:01: 14000000 INFO @ Wed, 08 Dec 2021 21:33:01: #2 number of paired peaks: 170 WARNING @ Wed, 08 Dec 2021 21:33:01: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Wed, 08 Dec 2021 21:33:01: start model_add_line... INFO @ Wed, 08 Dec 2021 21:33:02: start X-correlation... INFO @ Wed, 08 Dec 2021 21:33:02: end of X-cor INFO @ Wed, 08 Dec 2021 21:33:02: #2 finished! INFO @ Wed, 08 Dec 2021 21:33:02: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:33:02: #2 alternative fragment length(s) may be 1,45,154,499,534,567 bps INFO @ Wed, 08 Dec 2021 21:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.05_model.r WARNING @ Wed, 08 Dec 2021 21:33:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:33:02: #2 You may need to consider one of the other alternative d(s): 1,45,154,499,534,567 WARNING @ Wed, 08 Dec 2021 21:33:02: #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 21:33:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:33:05: 20000000 INFO @ Wed, 08 Dec 2021 21:33:07: 15000000 INFO @ Wed, 08 Dec 2021 21:33:11: 21000000 INFO @ Wed, 08 Dec 2021 21:33:13: 16000000 INFO @ Wed, 08 Dec 2021 21:33:16: 22000000 INFO @ Wed, 08 Dec 2021 21:33:19: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:33:22: 23000000 INFO @ Wed, 08 Dec 2021 21:33:24: 18000000 INFO @ Wed, 08 Dec 2021 21:33:28: 24000000 INFO @ Wed, 08 Dec 2021 21:33:30: 19000000 INFO @ Wed, 08 Dec 2021 21:33:33: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:33:33: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:33:33: #1 total tags in treatment: 24860992 INFO @ Wed, 08 Dec 2021 21:33:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:33:33: #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 21:33:33: #1 tags after filtering in treatment: 24860992 INFO @ Wed, 08 Dec 2021 21:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:33:33: #1 finished! INFO @ Wed, 08 Dec 2021 21:33:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:33:35: #2 number of paired peaks: 170 WARNING @ Wed, 08 Dec 2021 21:33:35: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Wed, 08 Dec 2021 21:33:35: start model_add_line... INFO @ Wed, 08 Dec 2021 21:33:35: start X-correlation... INFO @ Wed, 08 Dec 2021 21:33:35: end of X-cor INFO @ Wed, 08 Dec 2021 21:33:35: #2 finished! INFO @ Wed, 08 Dec 2021 21:33:35: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:33:35: #2 alternative fragment length(s) may be 1,45,154,499,534,567 bps INFO @ Wed, 08 Dec 2021 21:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.10_model.r WARNING @ Wed, 08 Dec 2021 21:33:35: #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 21:33:35: #2 You may need to consider one of the other alternative d(s): 1,45,154,499,534,567 WARNING @ Wed, 08 Dec 2021 21:33:35: #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 21:33:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:33:36: 20000000 INFO @ Wed, 08 Dec 2021 21:33:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:33:41: 21000000 INFO @ Wed, 08 Dec 2021 21:33:46: 22000000 INFO @ Wed, 08 Dec 2021 21:33:52: 23000000 INFO @ Wed, 08 Dec 2021 21:33:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:33:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:33:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.05_summits.bed INFO @ Wed, 08 Dec 2021 21:33:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:33:57: 24000000 INFO @ Wed, 08 Dec 2021 21:34:02: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:34:02: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:34:02: #1 total tags in treatment: 24860992 INFO @ Wed, 08 Dec 2021 21:34:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:34:02: #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 21:34:02: #1 tags after filtering in treatment: 24860992 INFO @ Wed, 08 Dec 2021 21:34:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:34:02: #1 finished! INFO @ Wed, 08 Dec 2021 21:34:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:34:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:34:03: #2 number of paired peaks: 170 WARNING @ Wed, 08 Dec 2021 21:34:03: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Wed, 08 Dec 2021 21:34:03: start model_add_line... INFO @ Wed, 08 Dec 2021 21:34:04: start X-correlation... INFO @ Wed, 08 Dec 2021 21:34:04: end of X-cor INFO @ Wed, 08 Dec 2021 21:34:04: #2 finished! INFO @ Wed, 08 Dec 2021 21:34:04: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:34:04: #2 alternative fragment length(s) may be 1,45,154,499,534,567 bps INFO @ Wed, 08 Dec 2021 21:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.20_model.r WARNING @ Wed, 08 Dec 2021 21:34:04: #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 21:34:04: #2 You may need to consider one of the other alternative d(s): 1,45,154,499,534,567 WARNING @ Wed, 08 Dec 2021 21:34:04: #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 21:34:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:34:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.10_summits.bed INFO @ Wed, 08 Dec 2021 21:34:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:34:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120609/SRX9120609.20_summits.bed INFO @ Wed, 08 Dec 2021 21:34:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling