Job ID = 14158197 SRX = SRX10641204 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED 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: 00:20:42 16930433 reads; of these: 16930433 (100.00%) were paired; of these: 11251118 (66.45%) aligned concordantly 0 times 4776625 (28.21%) aligned concordantly exactly 1 time 902690 (5.33%) aligned concordantly >1 times ---- 11251118 pairs aligned concordantly 0 times; of these: 2602062 (23.13%) aligned discordantly 1 time ---- 8649056 pairs aligned 0 times concordantly or discordantly; of these: 17298112 mates make up the pairs; of these: 15947108 (92.19%) aligned 0 times 710773 (4.11%) aligned exactly 1 time 640231 (3.70%) aligned >1 times 52.90% overall alignment rate Time searching: 00:20:42 Overall time: 00:20:42 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1037783 / 8260162 = 0.1256 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 15:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.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 15:12:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:12:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:12:44: 1000000 INFO @ Wed, 08 Dec 2021 15:12:52: 2000000 INFO @ Wed, 08 Dec 2021 15:13:00: 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 15:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.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 15:13:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:13:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:13:08: 4000000 INFO @ Wed, 08 Dec 2021 15:13:15: 1000000 INFO @ Wed, 08 Dec 2021 15:13:18: 5000000 INFO @ Wed, 08 Dec 2021 15:13:25: 2000000 INFO @ Wed, 08 Dec 2021 15:13:28: 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 15:13:35: 3000000 INFO @ Wed, 08 Dec 2021 15:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.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 15:13:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:13:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:13:38: 7000000 INFO @ Wed, 08 Dec 2021 15:13:46: 4000000 INFO @ Wed, 08 Dec 2021 15:13:47: 1000000 INFO @ Wed, 08 Dec 2021 15:13:49: 8000000 INFO @ Wed, 08 Dec 2021 15:13:57: 5000000 INFO @ Wed, 08 Dec 2021 15:13:59: 2000000 INFO @ Wed, 08 Dec 2021 15:14:00: 9000000 INFO @ Wed, 08 Dec 2021 15:14:08: 6000000 INFO @ Wed, 08 Dec 2021 15:14:11: 3000000 INFO @ Wed, 08 Dec 2021 15:14:11: 10000000 INFO @ Wed, 08 Dec 2021 15:14:19: 7000000 INFO @ Wed, 08 Dec 2021 15:14:23: 11000000 INFO @ Wed, 08 Dec 2021 15:14:23: 4000000 INFO @ Wed, 08 Dec 2021 15:14:31: 8000000 INFO @ Wed, 08 Dec 2021 15:14:34: 12000000 INFO @ Wed, 08 Dec 2021 15:14:35: 5000000 INFO @ Wed, 08 Dec 2021 15:14:42: 9000000 INFO @ Wed, 08 Dec 2021 15:14:45: 13000000 INFO @ Wed, 08 Dec 2021 15:14:47: 6000000 INFO @ Wed, 08 Dec 2021 15:14:54: 10000000 INFO @ Wed, 08 Dec 2021 15:14:57: 14000000 INFO @ Wed, 08 Dec 2021 15:14:59: 7000000 INFO @ Wed, 08 Dec 2021 15:15:05: 11000000 INFO @ Wed, 08 Dec 2021 15:15:09: 15000000 INFO @ Wed, 08 Dec 2021 15:15:10: 8000000 INFO @ Wed, 08 Dec 2021 15:15:16: 12000000 INFO @ Wed, 08 Dec 2021 15:15:18: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:15:18: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:15:18: #1 total tags in treatment: 4897754 INFO @ Wed, 08 Dec 2021 15:15:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:15:18: #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 15:15:18: #1 tags after filtering in treatment: 4562916 INFO @ Wed, 08 Dec 2021 15:15:18: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:15:18: #1 finished! INFO @ Wed, 08 Dec 2021 15:15:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:15:19: #2 number of paired peaks: 527 WARNING @ Wed, 08 Dec 2021 15:15:19: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Wed, 08 Dec 2021 15:15:19: start model_add_line... INFO @ Wed, 08 Dec 2021 15:15:19: start X-correlation... INFO @ Wed, 08 Dec 2021 15:15:19: end of X-cor INFO @ Wed, 08 Dec 2021 15:15:19: #2 finished! INFO @ Wed, 08 Dec 2021 15:15:19: #2 predicted fragment length is 218 bps INFO @ Wed, 08 Dec 2021 15:15:19: #2 alternative fragment length(s) may be 218 bps INFO @ Wed, 08 Dec 2021 15:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.05_model.r WARNING @ Wed, 08 Dec 2021 15:15:19: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:15:19: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Wed, 08 Dec 2021 15:15:19: #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 15:15:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:15:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:15:22: 9000000 INFO @ Wed, 08 Dec 2021 15:15:26: 13000000 INFO @ Wed, 08 Dec 2021 15:15:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:15:33: 10000000 INFO @ Wed, 08 Dec 2021 15:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.05_summits.bed INFO @ Wed, 08 Dec 2021 15:15:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:15:38: 14000000 INFO @ Wed, 08 Dec 2021 15:15:45: 11000000 INFO @ Wed, 08 Dec 2021 15:15:48: 15000000 INFO @ Wed, 08 Dec 2021 15:15:55: 12000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:15:57: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:15:57: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:15:57: #1 total tags in treatment: 4897754 INFO @ Wed, 08 Dec 2021 15:15:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:15:57: #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 15:15:58: #1 tags after filtering in treatment: 4562916 INFO @ Wed, 08 Dec 2021 15:15:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:15:58: #1 finished! INFO @ Wed, 08 Dec 2021 15:15:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:15:58: #2 number of paired peaks: 527 WARNING @ Wed, 08 Dec 2021 15:15:58: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Wed, 08 Dec 2021 15:15:58: start model_add_line... INFO @ Wed, 08 Dec 2021 15:15:58: start X-correlation... INFO @ Wed, 08 Dec 2021 15:15:58: end of X-cor INFO @ Wed, 08 Dec 2021 15:15:58: #2 finished! INFO @ Wed, 08 Dec 2021 15:15:58: #2 predicted fragment length is 218 bps INFO @ Wed, 08 Dec 2021 15:15:58: #2 alternative fragment length(s) may be 218 bps INFO @ Wed, 08 Dec 2021 15:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.10_model.r WARNING @ Wed, 08 Dec 2021 15:15:58: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:15:58: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Wed, 08 Dec 2021 15:15:58: #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 15:15:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:16:05: 13000000 INFO @ Wed, 08 Dec 2021 15:16:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:16:15: 14000000 INFO @ Wed, 08 Dec 2021 15:16:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:16:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:16:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.10_summits.bed INFO @ Wed, 08 Dec 2021 15:16:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:16:24: 15000000 INFO @ Wed, 08 Dec 2021 15:16:33: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:16:33: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:16:33: #1 total tags in treatment: 4897754 INFO @ Wed, 08 Dec 2021 15:16:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:16:33: #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 15:16:33: #1 tags after filtering in treatment: 4562916 INFO @ Wed, 08 Dec 2021 15:16:33: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:16:33: #1 finished! INFO @ Wed, 08 Dec 2021 15:16:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:16:33: #2 number of paired peaks: 527 WARNING @ Wed, 08 Dec 2021 15:16:33: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Wed, 08 Dec 2021 15:16:33: start model_add_line... INFO @ Wed, 08 Dec 2021 15:16:33: start X-correlation... INFO @ Wed, 08 Dec 2021 15:16:33: end of X-cor INFO @ Wed, 08 Dec 2021 15:16:33: #2 finished! INFO @ Wed, 08 Dec 2021 15:16:33: #2 predicted fragment length is 218 bps INFO @ Wed, 08 Dec 2021 15:16:33: #2 alternative fragment length(s) may be 218 bps INFO @ Wed, 08 Dec 2021 15:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.20_model.r WARNING @ Wed, 08 Dec 2021 15:16:33: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:16:33: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Wed, 08 Dec 2021 15:16:33: #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 15:16:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:16:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641204/SRX10641204.20_summits.bed INFO @ Wed, 08 Dec 2021 15:16:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 millis CompletedMACS2peakCalling