Job ID = 14158386 SRX = SRX10641219 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: 00:25:07 16788522 reads; of these: 16788522 (100.00%) were paired; of these: 8137938 (48.47%) aligned concordantly 0 times 7331868 (43.67%) aligned concordantly exactly 1 time 1318716 (7.85%) aligned concordantly >1 times ---- 8137938 pairs aligned concordantly 0 times; of these: 1915186 (23.53%) aligned discordantly 1 time ---- 6222752 pairs aligned 0 times concordantly or discordantly; of these: 12445504 mates make up the pairs; of these: 11593055 (93.15%) aligned 0 times 432753 (3.48%) aligned exactly 1 time 419696 (3.37%) aligned >1 times 65.47% overall alignment rate Time searching: 00:25:07 Overall time: 00:25:07 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] 1278950 / 10522187 = 0.1215 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 17:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.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 17:22:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:22:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:22:13: 1000000 INFO @ Wed, 08 Dec 2021 17:22:21: 2000000 INFO @ Wed, 08 Dec 2021 17:22:30: 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 17:22:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.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 17:22:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:22:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:22:39: 4000000 INFO @ Wed, 08 Dec 2021 17:22:45: 1000000 INFO @ Wed, 08 Dec 2021 17:22:49: 5000000 INFO @ Wed, 08 Dec 2021 17:22:55: 2000000 INFO @ Wed, 08 Dec 2021 17:22:59: 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 17:23:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.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 17:23:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:23:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:23:06: 3000000 INFO @ Wed, 08 Dec 2021 17:23:10: 7000000 INFO @ Wed, 08 Dec 2021 17:23:17: 1000000 INFO @ Wed, 08 Dec 2021 17:23:18: 4000000 INFO @ Wed, 08 Dec 2021 17:23:22: 8000000 INFO @ Wed, 08 Dec 2021 17:23:30: 5000000 INFO @ Wed, 08 Dec 2021 17:23:30: 2000000 INFO @ Wed, 08 Dec 2021 17:23:34: 9000000 INFO @ Wed, 08 Dec 2021 17:23:42: 6000000 INFO @ Wed, 08 Dec 2021 17:23:43: 3000000 INFO @ Wed, 08 Dec 2021 17:23:46: 10000000 INFO @ Wed, 08 Dec 2021 17:23:54: 7000000 INFO @ Wed, 08 Dec 2021 17:23:56: 4000000 INFO @ Wed, 08 Dec 2021 17:23:58: 11000000 INFO @ Wed, 08 Dec 2021 17:24:06: 8000000 INFO @ Wed, 08 Dec 2021 17:24:09: 5000000 INFO @ Wed, 08 Dec 2021 17:24:10: 12000000 INFO @ Wed, 08 Dec 2021 17:24:18: 9000000 INFO @ Wed, 08 Dec 2021 17:24:21: 6000000 INFO @ Wed, 08 Dec 2021 17:24:22: 13000000 INFO @ Wed, 08 Dec 2021 17:24:30: 10000000 INFO @ Wed, 08 Dec 2021 17:24:34: 14000000 INFO @ Wed, 08 Dec 2021 17:24:34: 7000000 INFO @ Wed, 08 Dec 2021 17:24:42: 11000000 INFO @ Wed, 08 Dec 2021 17:24:46: 15000000 INFO @ Wed, 08 Dec 2021 17:24:47: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:24:54: 12000000 INFO @ Wed, 08 Dec 2021 17:24:58: 16000000 INFO @ Wed, 08 Dec 2021 17:25:00: 9000000 INFO @ Wed, 08 Dec 2021 17:25:06: 13000000 INFO @ Wed, 08 Dec 2021 17:25:10: 17000000 INFO @ Wed, 08 Dec 2021 17:25:13: 10000000 INFO @ Wed, 08 Dec 2021 17:25:18: 14000000 INFO @ Wed, 08 Dec 2021 17:25:22: 18000000 INFO @ Wed, 08 Dec 2021 17:25:26: 11000000 INFO @ Wed, 08 Dec 2021 17:25:30: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:25:34: 19000000 INFO @ Wed, 08 Dec 2021 17:25:39: 12000000 INFO @ Wed, 08 Dec 2021 17:25:39: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:25:39: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:25:39: #1 total tags in treatment: 7554104 INFO @ Wed, 08 Dec 2021 17:25:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:25:39: #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 17:25:39: #1 tags after filtering in treatment: 6932918 INFO @ Wed, 08 Dec 2021 17:25:39: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:25:39: #1 finished! INFO @ Wed, 08 Dec 2021 17:25:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:25:40: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 17:25:40: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 17:25:40: start model_add_line... INFO @ Wed, 08 Dec 2021 17:25:40: start X-correlation... INFO @ Wed, 08 Dec 2021 17:25:40: end of X-cor INFO @ Wed, 08 Dec 2021 17:25:40: #2 finished! INFO @ Wed, 08 Dec 2021 17:25:40: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:25:40: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:25:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.05_model.r WARNING @ Wed, 08 Dec 2021 17:25:40: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:25:40: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:25:40: #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 17:25:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:25:41: 16000000 INFO @ Wed, 08 Dec 2021 17:25:52: 13000000 INFO @ Wed, 08 Dec 2021 17:25:53: 17000000 INFO @ Wed, 08 Dec 2021 17:25:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.05_summits.bed INFO @ Wed, 08 Dec 2021 17:26:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:26:04: 14000000 INFO @ Wed, 08 Dec 2021 17:26:05: 18000000 INFO @ Wed, 08 Dec 2021 17:26:16: 19000000 INFO @ Wed, 08 Dec 2021 17:26:17: 15000000 INFO @ Wed, 08 Dec 2021 17:26:21: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:26:21: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:26:21: #1 total tags in treatment: 7554104 INFO @ Wed, 08 Dec 2021 17:26:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:26:21: #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 17:26:21: #1 tags after filtering in treatment: 6932918 INFO @ Wed, 08 Dec 2021 17:26:21: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:26:21: #1 finished! INFO @ Wed, 08 Dec 2021 17:26:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:26:22: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 17:26:22: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 17:26:22: start model_add_line... INFO @ Wed, 08 Dec 2021 17:26:22: start X-correlation... INFO @ Wed, 08 Dec 2021 17:26:22: end of X-cor INFO @ Wed, 08 Dec 2021 17:26:22: #2 finished! INFO @ Wed, 08 Dec 2021 17:26:22: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:26:22: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.10_model.r WARNING @ Wed, 08 Dec 2021 17:26:22: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:26:22: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:26:22: #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 17:26:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:26:27: 16000000 INFO @ Wed, 08 Dec 2021 17:26:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:26:38: 17000000 INFO @ Wed, 08 Dec 2021 17:26:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:26:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:26:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.10_summits.bed INFO @ Wed, 08 Dec 2021 17:26:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:26:50: 18000000 INFO @ Wed, 08 Dec 2021 17:27:01: 19000000 INFO @ Wed, 08 Dec 2021 17:27:06: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:27:06: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:27:06: #1 total tags in treatment: 7554104 INFO @ Wed, 08 Dec 2021 17:27:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:27:06: #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 17:27:06: #1 tags after filtering in treatment: 6932918 INFO @ Wed, 08 Dec 2021 17:27:06: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:27:06: #1 finished! INFO @ Wed, 08 Dec 2021 17:27:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:27:07: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 17:27:07: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 17:27:07: start model_add_line... INFO @ Wed, 08 Dec 2021 17:27:07: start X-correlation... INFO @ Wed, 08 Dec 2021 17:27:07: end of X-cor INFO @ Wed, 08 Dec 2021 17:27:07: #2 finished! INFO @ Wed, 08 Dec 2021 17:27:07: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:27:07: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.20_model.r WARNING @ Wed, 08 Dec 2021 17:27:07: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:27:07: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:27:07: #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 17:27:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:27:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641219/SRX10641219.20_summits.bed INFO @ Wed, 08 Dec 2021 17:27:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 1 millis CompletedMACS2peakCalling