Job ID = 14158994 SRX = SRX10641176 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: 00:00:01 Multiseed full-index search: 00:31:00 14155663 reads; of these: 14155663 (100.00%) were paired; of these: 7539224 (53.26%) aligned concordantly 0 times 5570775 (39.35%) aligned concordantly exactly 1 time 1045664 (7.39%) aligned concordantly >1 times ---- 7539224 pairs aligned concordantly 0 times; of these: 2144089 (28.44%) aligned discordantly 1 time ---- 5395135 pairs aligned 0 times concordantly or discordantly; of these: 10790270 mates make up the pairs; of these: 9805470 (90.87%) aligned 0 times 501135 (4.64%) aligned exactly 1 time 483665 (4.48%) aligned >1 times 65.37% overall alignment rate Time searching: 00:31:01 Overall time: 00:31:01 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] 1046457 / 8733851 = 0.1198 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 19:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.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 19:17:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:17:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:18:00: 1000000 INFO @ Wed, 08 Dec 2021 19:18:12: 2000000 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 19:18:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.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 19:18:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:18:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:18:25: 3000000 INFO @ Wed, 08 Dec 2021 19:18:31: 1000000 INFO @ Wed, 08 Dec 2021 19:18:38: 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 19:18:45: 2000000 INFO @ Wed, 08 Dec 2021 19:18:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.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 19:18:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:18:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:18:51: 5000000 INFO @ Wed, 08 Dec 2021 19:19:00: 3000000 INFO @ Wed, 08 Dec 2021 19:19:04: 1000000 INFO @ Wed, 08 Dec 2021 19:19:05: 6000000 INFO @ Wed, 08 Dec 2021 19:19:15: 4000000 INFO @ Wed, 08 Dec 2021 19:19:18: 7000000 INFO @ Wed, 08 Dec 2021 19:19:22: 2000000 INFO @ Wed, 08 Dec 2021 19:19:30: 5000000 INFO @ Wed, 08 Dec 2021 19:19:31: 8000000 INFO @ Wed, 08 Dec 2021 19:19:38: 3000000 INFO @ Wed, 08 Dec 2021 19:19:44: 6000000 INFO @ Wed, 08 Dec 2021 19:19:45: 9000000 INFO @ Wed, 08 Dec 2021 19:19:53: 4000000 INFO @ Wed, 08 Dec 2021 19:19:58: 7000000 INFO @ Wed, 08 Dec 2021 19:20:00: 10000000 INFO @ Wed, 08 Dec 2021 19:20:08: 5000000 INFO @ Wed, 08 Dec 2021 19:20:12: 8000000 INFO @ Wed, 08 Dec 2021 19:20:14: 11000000 INFO @ Wed, 08 Dec 2021 19:20:24: 6000000 INFO @ Wed, 08 Dec 2021 19:20:26: 9000000 INFO @ Wed, 08 Dec 2021 19:20:28: 12000000 INFO @ Wed, 08 Dec 2021 19:20:40: 7000000 INFO @ Wed, 08 Dec 2021 19:20:40: 10000000 INFO @ Wed, 08 Dec 2021 19:20:43: 13000000 INFO @ Wed, 08 Dec 2021 19:20:54: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:20:56: 8000000 INFO @ Wed, 08 Dec 2021 19:20:57: 14000000 INFO @ Wed, 08 Dec 2021 19:21:07: 12000000 INFO @ Wed, 08 Dec 2021 19:21:12: 15000000 INFO @ Wed, 08 Dec 2021 19:21:12: 9000000 INFO @ Wed, 08 Dec 2021 19:21:21: 13000000 INFO @ Wed, 08 Dec 2021 19:21:27: 16000000 INFO @ Wed, 08 Dec 2021 19:21:29: 10000000 INFO @ Wed, 08 Dec 2021 19:21:34: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:21:34: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:21:34: #1 total tags in treatment: 5765510 INFO @ Wed, 08 Dec 2021 19:21:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:21:34: #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 19:21:34: #1 tags after filtering in treatment: 5320487 INFO @ Wed, 08 Dec 2021 19:21:34: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:21:34: #1 finished! INFO @ Wed, 08 Dec 2021 19:21:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:21:34: #2 number of paired peaks: 601 WARNING @ Wed, 08 Dec 2021 19:21:34: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Wed, 08 Dec 2021 19:21:34: start model_add_line... INFO @ Wed, 08 Dec 2021 19:21:34: 14000000 INFO @ Wed, 08 Dec 2021 19:21:34: start X-correlation... INFO @ Wed, 08 Dec 2021 19:21:34: end of X-cor INFO @ Wed, 08 Dec 2021 19:21:34: #2 finished! INFO @ Wed, 08 Dec 2021 19:21:34: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 19:21:34: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 19:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.05_model.r WARNING @ Wed, 08 Dec 2021 19:21:34: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:21:34: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 19:21:34: #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 19:21:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:21:44: 11000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:21:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:21:48: 15000000 INFO @ Wed, 08 Dec 2021 19:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.05_summits.bed INFO @ Wed, 08 Dec 2021 19:21:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:21:59: 12000000 INFO @ Wed, 08 Dec 2021 19:22:01: 16000000 INFO @ Wed, 08 Dec 2021 19:22:07: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:22:07: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:22:07: #1 total tags in treatment: 5765510 INFO @ Wed, 08 Dec 2021 19:22:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:22:07: #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 19:22:07: #1 tags after filtering in treatment: 5320487 INFO @ Wed, 08 Dec 2021 19:22:07: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:22:07: #1 finished! INFO @ Wed, 08 Dec 2021 19:22:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:22:08: #2 number of paired peaks: 601 WARNING @ Wed, 08 Dec 2021 19:22:08: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Wed, 08 Dec 2021 19:22:08: start model_add_line... INFO @ Wed, 08 Dec 2021 19:22:08: start X-correlation... INFO @ Wed, 08 Dec 2021 19:22:08: end of X-cor INFO @ Wed, 08 Dec 2021 19:22:08: #2 finished! INFO @ Wed, 08 Dec 2021 19:22:08: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 19:22:08: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 19:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.10_model.r WARNING @ Wed, 08 Dec 2021 19:22:08: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:22:08: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 19:22:08: #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 19:22:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:22:15: 13000000 INFO @ Wed, 08 Dec 2021 19:22:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.10_summits.bed INFO @ Wed, 08 Dec 2021 19:22:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:22:30: 14000000 INFO @ Wed, 08 Dec 2021 19:22:45: 15000000 INFO @ Wed, 08 Dec 2021 19:23:00: 16000000 INFO @ Wed, 08 Dec 2021 19:23:06: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:23:06: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:23:06: #1 total tags in treatment: 5765510 INFO @ Wed, 08 Dec 2021 19:23:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:23:06: #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 19:23:06: #1 tags after filtering in treatment: 5320487 INFO @ Wed, 08 Dec 2021 19:23:06: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:23:06: #1 finished! INFO @ Wed, 08 Dec 2021 19:23:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:23:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:23:06: #2 number of paired peaks: 601 WARNING @ Wed, 08 Dec 2021 19:23:06: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Wed, 08 Dec 2021 19:23:06: start model_add_line... INFO @ Wed, 08 Dec 2021 19:23:07: start X-correlation... INFO @ Wed, 08 Dec 2021 19:23:07: end of X-cor INFO @ Wed, 08 Dec 2021 19:23:07: #2 finished! INFO @ Wed, 08 Dec 2021 19:23:07: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 19:23:07: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 19:23:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.20_model.r WARNING @ Wed, 08 Dec 2021 19:23:07: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:23:07: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 19:23:07: #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 19:23:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:23:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641176/SRX10641176.20_summits.bed INFO @ Wed, 08 Dec 2021 19:23:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 2 millis CompletedMACS2peakCalling