Job ID = 14159410 SRX = SRX9120615 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:31 22488133 reads; of these: 22488133 (100.00%) were unpaired; of these: 712449 (3.17%) aligned 0 times 18191071 (80.89%) aligned exactly 1 time 3584613 (15.94%) aligned >1 times 96.83% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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 12 files... [bam_rmdupse_core] 3064742 / 21775684 = 0.1407 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 21:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.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 21:43:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:43:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:43:45: 1000000 INFO @ Wed, 08 Dec 2021 21:43:52: 2000000 INFO @ Wed, 08 Dec 2021 21:43:59: 3000000 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 21:44:06: 4000000 INFO @ Wed, 08 Dec 2021 21:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.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 21:44:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:44:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:44:13: 5000000 INFO @ Wed, 08 Dec 2021 21:44:17: 1000000 INFO @ Wed, 08 Dec 2021 21:44:20: 6000000 INFO @ Wed, 08 Dec 2021 21:44:26: 2000000 INFO @ Wed, 08 Dec 2021 21:44:27: 7000000 INFO @ Wed, 08 Dec 2021 21:44:34: 8000000 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 21:44:35: 3000000 INFO @ Wed, 08 Dec 2021 21:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.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 21:44:37: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:44:37: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:44:41: 9000000 INFO @ Wed, 08 Dec 2021 21:44:44: 4000000 INFO @ Wed, 08 Dec 2021 21:44:45: 1000000 INFO @ Wed, 08 Dec 2021 21:44:48: 10000000 INFO @ Wed, 08 Dec 2021 21:44:52: 2000000 INFO @ Wed, 08 Dec 2021 21:44:53: 5000000 INFO @ Wed, 08 Dec 2021 21:44:55: 11000000 INFO @ Wed, 08 Dec 2021 21:44:59: 3000000 INFO @ Wed, 08 Dec 2021 21:45:02: 6000000 INFO @ Wed, 08 Dec 2021 21:45:03: 12000000 INFO @ Wed, 08 Dec 2021 21:45:06: 4000000 INFO @ Wed, 08 Dec 2021 21:45:10: 13000000 INFO @ Wed, 08 Dec 2021 21:45:11: 7000000 INFO @ Wed, 08 Dec 2021 21:45:13: 5000000 INFO @ Wed, 08 Dec 2021 21:45:16: 14000000 INFO @ Wed, 08 Dec 2021 21:45:20: 8000000 INFO @ Wed, 08 Dec 2021 21:45:20: 6000000 INFO @ Wed, 08 Dec 2021 21:45:24: 15000000 INFO @ Wed, 08 Dec 2021 21:45:28: 7000000 INFO @ Wed, 08 Dec 2021 21:45:29: 9000000 INFO @ Wed, 08 Dec 2021 21:45:32: 16000000 INFO @ Wed, 08 Dec 2021 21:45:36: 8000000 INFO @ Wed, 08 Dec 2021 21:45:39: 10000000 INFO @ Wed, 08 Dec 2021 21:45:40: 17000000 INFO @ Wed, 08 Dec 2021 21:45:44: 9000000 INFO @ Wed, 08 Dec 2021 21:45:48: 18000000 INFO @ Wed, 08 Dec 2021 21:45:48: 11000000 INFO @ Wed, 08 Dec 2021 21:45:52: 10000000 INFO @ Wed, 08 Dec 2021 21:45:54: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:45:54: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:45:54: #1 total tags in treatment: 18710942 INFO @ Wed, 08 Dec 2021 21:45:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:45:54: #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 21:45:54: #1 tags after filtering in treatment: 18710942 INFO @ Wed, 08 Dec 2021 21:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:45:54: #1 finished! INFO @ Wed, 08 Dec 2021 21:45:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:45:55: #2 number of paired peaks: 205 WARNING @ Wed, 08 Dec 2021 21:45:55: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Wed, 08 Dec 2021 21:45:55: start model_add_line... INFO @ Wed, 08 Dec 2021 21:45:56: start X-correlation... INFO @ Wed, 08 Dec 2021 21:45:56: end of X-cor INFO @ Wed, 08 Dec 2021 21:45:56: #2 finished! INFO @ Wed, 08 Dec 2021 21:45:56: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:45:56: #2 alternative fragment length(s) may be 1,14,38,46,537 bps INFO @ Wed, 08 Dec 2021 21:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_model.r WARNING @ Wed, 08 Dec 2021 21:45:56: #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 21:45:56: #2 You may need to consider one of the other alternative d(s): 1,14,38,46,537 WARNING @ Wed, 08 Dec 2021 21:45:56: #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 21:45:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:45:57: 12000000 INFO @ Wed, 08 Dec 2021 21:45:59: 11000000 INFO @ Wed, 08 Dec 2021 21:46:06: 13000000 INFO @ Wed, 08 Dec 2021 21:46:07: 12000000 INFO @ Wed, 08 Dec 2021 21:46:14: 13000000 INFO @ Wed, 08 Dec 2021 21:46:15: 14000000 INFO @ Wed, 08 Dec 2021 21:46:20: 14000000 INFO @ Wed, 08 Dec 2021 21:46:24: 15000000 INFO @ Wed, 08 Dec 2021 21:46:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:46:33: 16000000 INFO @ Wed, 08 Dec 2021 21:46:34: 16000000 INFO @ Wed, 08 Dec 2021 21:46:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:46:41: 17000000 INFO @ Wed, 08 Dec 2021 21:46:42: 17000000 INFO @ Wed, 08 Dec 2021 21:46:48: 18000000 INFO @ Wed, 08 Dec 2021 21:46:51: 18000000 INFO @ Wed, 08 Dec 2021 21:46:53: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:46:53: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:46:53: #1 total tags in treatment: 18710942 INFO @ Wed, 08 Dec 2021 21:46:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:46:53: #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 21:46:54: #1 tags after filtering in treatment: 18710942 INFO @ Wed, 08 Dec 2021 21:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:46:54: #1 finished! INFO @ Wed, 08 Dec 2021 21:46:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:46:55: #2 number of paired peaks: 205 WARNING @ Wed, 08 Dec 2021 21:46:55: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Wed, 08 Dec 2021 21:46:55: start model_add_line... INFO @ Wed, 08 Dec 2021 21:46:55: start X-correlation... INFO @ Wed, 08 Dec 2021 21:46:55: end of X-cor INFO @ Wed, 08 Dec 2021 21:46:55: #2 finished! INFO @ Wed, 08 Dec 2021 21:46:55: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:46:55: #2 alternative fragment length(s) may be 1,14,38,46,537 bps INFO @ Wed, 08 Dec 2021 21:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_model.r WARNING @ Wed, 08 Dec 2021 21:46:55: #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 21:46:55: #2 You may need to consider one of the other alternative d(s): 1,14,38,46,537 WARNING @ Wed, 08 Dec 2021 21:46:55: #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 21:46:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_summits.bed INFO @ Wed, 08 Dec 2021 21:46:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:46:57: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:46:57: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:46:57: #1 total tags in treatment: 18710942 INFO @ Wed, 08 Dec 2021 21:46:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:46:57: #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 21:46:57: #1 tags after filtering in treatment: 18710942 INFO @ Wed, 08 Dec 2021 21:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:46:57: #1 finished! INFO @ Wed, 08 Dec 2021 21:46:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:46:59: #2 number of paired peaks: 205 WARNING @ Wed, 08 Dec 2021 21:46:59: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Wed, 08 Dec 2021 21:46:59: start model_add_line... INFO @ Wed, 08 Dec 2021 21:46:59: start X-correlation... INFO @ Wed, 08 Dec 2021 21:46:59: end of X-cor INFO @ Wed, 08 Dec 2021 21:46:59: #2 finished! INFO @ Wed, 08 Dec 2021 21:46:59: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:46:59: #2 alternative fragment length(s) may be 1,14,38,46,537 bps INFO @ Wed, 08 Dec 2021 21:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_model.r WARNING @ Wed, 08 Dec 2021 21:46:59: #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 21:46:59: #2 You may need to consider one of the other alternative d(s): 1,14,38,46,537 WARNING @ Wed, 08 Dec 2021 21:46:59: #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 21:46:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:46:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:47:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:47:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:47:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:47:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_summits.bed INFO @ Wed, 08 Dec 2021 21:47:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_summits.bed INFO @ Wed, 08 Dec 2021 21:47:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling