Job ID = 14159696 SRX = SRX8845631 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: 00:06:54 49002203 reads; of these: 49002203 (100.00%) were unpaired; of these: 24832188 (50.68%) aligned 0 times 19875066 (40.56%) aligned exactly 1 time 4294949 (8.76%) aligned >1 times 49.32% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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 12 files... [bam_rmdupse_core] 3098959 / 24170015 = 0.1282 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 @ Thu, 09 Dec 2021 00:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.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 @ Thu, 09 Dec 2021 00:35:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:35:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:35:58: 1000000 INFO @ Thu, 09 Dec 2021 00:36:05: 2000000 INFO @ Thu, 09 Dec 2021 00:36:12: 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 @ Thu, 09 Dec 2021 00:36:19: 4000000 INFO @ Thu, 09 Dec 2021 00:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.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 @ Thu, 09 Dec 2021 00:36:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:36:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:36:27: 5000000 INFO @ Thu, 09 Dec 2021 00:36:28: 1000000 INFO @ Thu, 09 Dec 2021 00:36:35: 6000000 INFO @ Thu, 09 Dec 2021 00:36:36: 2000000 INFO @ Thu, 09 Dec 2021 00:36:43: 7000000 INFO @ Thu, 09 Dec 2021 00:36:43: 3000000 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 @ Thu, 09 Dec 2021 00:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.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 @ Thu, 09 Dec 2021 00:36:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:36:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:36:51: 8000000 INFO @ Thu, 09 Dec 2021 00:36:51: 4000000 INFO @ Thu, 09 Dec 2021 00:36:59: 1000000 INFO @ Thu, 09 Dec 2021 00:36:59: 9000000 INFO @ Thu, 09 Dec 2021 00:36:59: 5000000 INFO @ Thu, 09 Dec 2021 00:37:07: 6000000 INFO @ Thu, 09 Dec 2021 00:37:07: 2000000 INFO @ Thu, 09 Dec 2021 00:37:07: 10000000 INFO @ Thu, 09 Dec 2021 00:37:14: 7000000 INFO @ Thu, 09 Dec 2021 00:37:15: 3000000 INFO @ Thu, 09 Dec 2021 00:37:15: 11000000 INFO @ Thu, 09 Dec 2021 00:37:22: 8000000 INFO @ Thu, 09 Dec 2021 00:37:23: 4000000 INFO @ Thu, 09 Dec 2021 00:37:23: 12000000 INFO @ Thu, 09 Dec 2021 00:37:30: 9000000 INFO @ Thu, 09 Dec 2021 00:37:31: 5000000 INFO @ Thu, 09 Dec 2021 00:37:31: 13000000 INFO @ Thu, 09 Dec 2021 00:37:38: 10000000 INFO @ Thu, 09 Dec 2021 00:37:39: 6000000 INFO @ Thu, 09 Dec 2021 00:37:39: 14000000 INFO @ Thu, 09 Dec 2021 00:37:46: 11000000 INFO @ Thu, 09 Dec 2021 00:37:47: 7000000 INFO @ Thu, 09 Dec 2021 00:37:47: 15000000 INFO @ Thu, 09 Dec 2021 00:37:53: 12000000 INFO @ Thu, 09 Dec 2021 00:37:55: 8000000 INFO @ Thu, 09 Dec 2021 00:37:55: 16000000 INFO @ Thu, 09 Dec 2021 00:38:01: 13000000 INFO @ Thu, 09 Dec 2021 00:38:03: 9000000 INFO @ Thu, 09 Dec 2021 00:38:04: 17000000 INFO @ Thu, 09 Dec 2021 00:38:09: 14000000 INFO @ Thu, 09 Dec 2021 00:38:11: 10000000 INFO @ Thu, 09 Dec 2021 00:38:12: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:38:17: 15000000 INFO @ Thu, 09 Dec 2021 00:38:19: 11000000 INFO @ Thu, 09 Dec 2021 00:38:20: 19000000 INFO @ Thu, 09 Dec 2021 00:38:24: 16000000 INFO @ Thu, 09 Dec 2021 00:38:27: 12000000 INFO @ Thu, 09 Dec 2021 00:38:28: 20000000 INFO @ Thu, 09 Dec 2021 00:38:32: 17000000 INFO @ Thu, 09 Dec 2021 00:38:35: 13000000 INFO @ Thu, 09 Dec 2021 00:38:36: 21000000 INFO @ Thu, 09 Dec 2021 00:38:37: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:38:37: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:38:37: #1 total tags in treatment: 21071056 INFO @ Thu, 09 Dec 2021 00:38:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:38:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:38:37: #1 tags after filtering in treatment: 21071056 INFO @ Thu, 09 Dec 2021 00:38:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:38:37: #1 finished! INFO @ Thu, 09 Dec 2021 00:38:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:38:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:38:39: #2 number of paired peaks: 174 WARNING @ Thu, 09 Dec 2021 00:38:39: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Thu, 09 Dec 2021 00:38:39: start model_add_line... INFO @ Thu, 09 Dec 2021 00:38:39: start X-correlation... INFO @ Thu, 09 Dec 2021 00:38:39: end of X-cor INFO @ Thu, 09 Dec 2021 00:38:39: #2 finished! INFO @ Thu, 09 Dec 2021 00:38:39: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 00:38:39: #2 alternative fragment length(s) may be 1,24,43 bps INFO @ Thu, 09 Dec 2021 00:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.05_model.r WARNING @ Thu, 09 Dec 2021 00:38:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:38:39: #2 You may need to consider one of the other alternative d(s): 1,24,43 WARNING @ Thu, 09 Dec 2021 00:38:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:38:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:38:40: 18000000 INFO @ Thu, 09 Dec 2021 00:38:43: 14000000 INFO @ Thu, 09 Dec 2021 00:38:47: 19000000 INFO @ Thu, 09 Dec 2021 00:38:50: 15000000 INFO @ Thu, 09 Dec 2021 00:38:55: 20000000 INFO @ Thu, 09 Dec 2021 00:38:58: 16000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:39:02: 21000000 INFO @ Thu, 09 Dec 2021 00:39:03: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:39:03: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:39:03: #1 total tags in treatment: 21071056 INFO @ Thu, 09 Dec 2021 00:39:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:39:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:39:03: #1 tags after filtering in treatment: 21071056 INFO @ Thu, 09 Dec 2021 00:39:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:39:03: #1 finished! INFO @ Thu, 09 Dec 2021 00:39:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:39:05: #2 number of paired peaks: 174 WARNING @ Thu, 09 Dec 2021 00:39:05: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Thu, 09 Dec 2021 00:39:05: start model_add_line... INFO @ Thu, 09 Dec 2021 00:39:05: start X-correlation... INFO @ Thu, 09 Dec 2021 00:39:05: end of X-cor INFO @ Thu, 09 Dec 2021 00:39:05: #2 finished! INFO @ Thu, 09 Dec 2021 00:39:05: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 00:39:05: #2 alternative fragment length(s) may be 1,24,43 bps INFO @ Thu, 09 Dec 2021 00:39:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.10_model.r WARNING @ Thu, 09 Dec 2021 00:39:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:39:05: #2 You may need to consider one of the other alternative d(s): 1,24,43 WARNING @ Thu, 09 Dec 2021 00:39:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:39:05: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:39:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:39:06: 17000000 INFO @ Thu, 09 Dec 2021 00:39:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:39:13: 18000000 INFO @ Thu, 09 Dec 2021 00:39:20: 19000000 INFO @ Thu, 09 Dec 2021 00:39:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:39:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.05_summits.bed INFO @ Thu, 09 Dec 2021 00:39:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:39:27: 20000000 INFO @ Thu, 09 Dec 2021 00:39:34: 21000000 INFO @ Thu, 09 Dec 2021 00:39:35: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:39:35: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:39:35: #1 total tags in treatment: 21071056 INFO @ Thu, 09 Dec 2021 00:39:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:39:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:39:35: #1 tags after filtering in treatment: 21071056 INFO @ Thu, 09 Dec 2021 00:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:39:35: #1 finished! INFO @ Thu, 09 Dec 2021 00:39:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:39:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:39:36: #2 number of paired peaks: 174 WARNING @ Thu, 09 Dec 2021 00:39:36: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Thu, 09 Dec 2021 00:39:36: start model_add_line... INFO @ Thu, 09 Dec 2021 00:39:36: start X-correlation... INFO @ Thu, 09 Dec 2021 00:39:36: end of X-cor INFO @ Thu, 09 Dec 2021 00:39:36: #2 finished! INFO @ Thu, 09 Dec 2021 00:39:36: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 00:39:36: #2 alternative fragment length(s) may be 1,24,43 bps INFO @ Thu, 09 Dec 2021 00:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.20_model.r WARNING @ Thu, 09 Dec 2021 00:39:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:39:36: #2 You may need to consider one of the other alternative d(s): 1,24,43 WARNING @ Thu, 09 Dec 2021 00:39:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:39:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.10_summits.bed INFO @ Thu, 09 Dec 2021 00:39:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:40:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:40:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:40:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:40:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845631/SRX8845631.20_summits.bed INFO @ Thu, 09 Dec 2021 00:40:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling