Job ID = 12265378 SRX = SRX3029132 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: 00:27:23 24717131 reads; of these: 24717131 (100.00%) were paired; of these: 7692415 (31.12%) aligned concordantly 0 times 14972656 (60.58%) aligned concordantly exactly 1 time 2052060 (8.30%) aligned concordantly >1 times ---- 7692415 pairs aligned concordantly 0 times; of these: 2164071 (28.13%) aligned discordantly 1 time ---- 5528344 pairs aligned 0 times concordantly or discordantly; of these: 11056688 mates make up the pairs; of these: 9929095 (89.80%) aligned 0 times 512230 (4.63%) aligned exactly 1 time 615363 (5.57%) aligned >1 times 79.91% overall alignment rate Time searching: 00:27:23 Overall time: 00:27:23 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 20 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] 5271186 / 19008213 = 0.2773 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:32:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.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 @ Sat, 03 Apr 2021 07:32:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:32:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:21: 1000000 INFO @ Sat, 03 Apr 2021 07:32:30: 2000000 INFO @ Sat, 03 Apr 2021 07:32:38: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:32:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.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 @ Sat, 03 Apr 2021 07:32:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:32:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:47: 4000000 INFO @ Sat, 03 Apr 2021 07:32:51: 1000000 INFO @ Sat, 03 Apr 2021 07:32:56: 5000000 INFO @ Sat, 03 Apr 2021 07:33:00: 2000000 INFO @ Sat, 03 Apr 2021 07:33:05: 6000000 INFO @ Sat, 03 Apr 2021 07:33:09: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.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 @ Sat, 03 Apr 2021 07:33:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:14: 7000000 INFO @ Sat, 03 Apr 2021 07:33:18: 4000000 INFO @ Sat, 03 Apr 2021 07:33:22: 1000000 INFO @ Sat, 03 Apr 2021 07:33:22: 8000000 INFO @ Sat, 03 Apr 2021 07:33:26: 5000000 INFO @ Sat, 03 Apr 2021 07:33:31: 2000000 INFO @ Sat, 03 Apr 2021 07:33:31: 9000000 INFO @ Sat, 03 Apr 2021 07:33:35: 6000000 INFO @ Sat, 03 Apr 2021 07:33:40: 3000000 INFO @ Sat, 03 Apr 2021 07:33:40: 10000000 INFO @ Sat, 03 Apr 2021 07:33:44: 7000000 INFO @ Sat, 03 Apr 2021 07:33:49: 11000000 INFO @ Sat, 03 Apr 2021 07:33:49: 4000000 INFO @ Sat, 03 Apr 2021 07:33:52: 8000000 INFO @ Sat, 03 Apr 2021 07:33:57: 12000000 INFO @ Sat, 03 Apr 2021 07:33:58: 5000000 INFO @ Sat, 03 Apr 2021 07:34:01: 9000000 INFO @ Sat, 03 Apr 2021 07:34:05: 13000000 INFO @ Sat, 03 Apr 2021 07:34:06: 6000000 INFO @ Sat, 03 Apr 2021 07:34:09: 10000000 INFO @ Sat, 03 Apr 2021 07:34:13: 14000000 INFO @ Sat, 03 Apr 2021 07:34:15: 7000000 INFO @ Sat, 03 Apr 2021 07:34:17: 11000000 INFO @ Sat, 03 Apr 2021 07:34:22: 15000000 INFO @ Sat, 03 Apr 2021 07:34:24: 8000000 INFO @ Sat, 03 Apr 2021 07:34:25: 12000000 INFO @ Sat, 03 Apr 2021 07:34:30: 16000000 INFO @ Sat, 03 Apr 2021 07:34:32: 9000000 INFO @ Sat, 03 Apr 2021 07:34:34: 13000000 INFO @ Sat, 03 Apr 2021 07:34:39: 17000000 INFO @ Sat, 03 Apr 2021 07:34:41: 10000000 INFO @ Sat, 03 Apr 2021 07:34:42: 14000000 INFO @ Sat, 03 Apr 2021 07:34:47: 18000000 INFO @ Sat, 03 Apr 2021 07:34:49: 11000000 INFO @ Sat, 03 Apr 2021 07:34:50: 15000000 INFO @ Sat, 03 Apr 2021 07:34:55: 19000000 INFO @ Sat, 03 Apr 2021 07:34:57: 12000000 INFO @ Sat, 03 Apr 2021 07:34:58: 16000000 INFO @ Sat, 03 Apr 2021 07:35:03: 20000000 INFO @ Sat, 03 Apr 2021 07:35:05: 13000000 INFO @ Sat, 03 Apr 2021 07:35:06: 17000000 INFO @ Sat, 03 Apr 2021 07:35:11: 21000000 INFO @ Sat, 03 Apr 2021 07:35:13: 14000000 INFO @ Sat, 03 Apr 2021 07:35:14: 18000000 INFO @ Sat, 03 Apr 2021 07:35:19: 22000000 INFO @ Sat, 03 Apr 2021 07:35:21: 15000000 INFO @ Sat, 03 Apr 2021 07:35:22: 19000000 INFO @ Sat, 03 Apr 2021 07:35:27: 23000000 INFO @ Sat, 03 Apr 2021 07:35:30: 16000000 INFO @ Sat, 03 Apr 2021 07:35:30: 20000000 INFO @ Sat, 03 Apr 2021 07:35:34: 24000000 INFO @ Sat, 03 Apr 2021 07:35:37: 21000000 INFO @ Sat, 03 Apr 2021 07:35:37: 17000000 INFO @ Sat, 03 Apr 2021 07:35:42: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:35:45: 22000000 INFO @ Sat, 03 Apr 2021 07:35:45: 18000000 INFO @ Sat, 03 Apr 2021 07:35:49: 26000000 INFO @ Sat, 03 Apr 2021 07:35:52: 23000000 INFO @ Sat, 03 Apr 2021 07:35:53: 19000000 INFO @ Sat, 03 Apr 2021 07:35:57: 27000000 INFO @ Sat, 03 Apr 2021 07:36:00: 24000000 INFO @ Sat, 03 Apr 2021 07:36:01: 20000000 INFO @ Sat, 03 Apr 2021 07:36:04: 28000000 INFO @ Sat, 03 Apr 2021 07:36:08: 25000000 INFO @ Sat, 03 Apr 2021 07:36:09: 21000000 INFO @ Sat, 03 Apr 2021 07:36:11: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:36:11: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:36:11: #1 total tags in treatment: 12280969 INFO @ Sat, 03 Apr 2021 07:36:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:36:11: #1 tags after filtering in treatment: 9145693 INFO @ Sat, 03 Apr 2021 07:36:11: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:36:11: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:12: #2 number of paired peaks: 529 WARNING @ Sat, 03 Apr 2021 07:36:12: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:12: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:12: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:12: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:12: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:12: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 07:36:12: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Apr 2021 07:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.05_model.r WARNING @ Sat, 03 Apr 2021 07:36:12: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:12: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sat, 03 Apr 2021 07:36:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:36:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:16: 26000000 INFO @ Sat, 03 Apr 2021 07:36:16: 22000000 INFO @ Sat, 03 Apr 2021 07:36:23: 27000000 INFO @ Sat, 03 Apr 2021 07:36:23: 23000000 INFO @ Sat, 03 Apr 2021 07:36:29: 28000000 INFO @ Sat, 03 Apr 2021 07:36:30: 24000000 INFO @ Sat, 03 Apr 2021 07:36:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:36: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:36:36: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:36:36: #1 total tags in treatment: 12280969 INFO @ Sat, 03 Apr 2021 07:36:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:36:36: #1 tags after filtering in treatment: 9145693 INFO @ Sat, 03 Apr 2021 07:36:36: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:36:36: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:37: #2 number of paired peaks: 529 WARNING @ Sat, 03 Apr 2021 07:36:37: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:37: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:37: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:37: 25000000 INFO @ Sat, 03 Apr 2021 07:36:37: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:37: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:37: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 07:36:37: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Apr 2021 07:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.10_model.r WARNING @ Sat, 03 Apr 2021 07:36:37: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:37: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sat, 03 Apr 2021 07:36:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:36:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.05_summits.bed INFO @ Sat, 03 Apr 2021 07:36:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6223 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:36:43: 26000000 INFO @ Sat, 03 Apr 2021 07:36:49: 27000000 INFO @ Sat, 03 Apr 2021 07:36:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:56: 28000000 INFO @ Sat, 03 Apr 2021 07:37:02: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:37:02: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:37:02: #1 total tags in treatment: 12280969 INFO @ Sat, 03 Apr 2021 07:37:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:37:02: #1 tags after filtering in treatment: 9145693 INFO @ Sat, 03 Apr 2021 07:37:02: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:37:02: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:03: #2 number of paired peaks: 529 WARNING @ Sat, 03 Apr 2021 07:37:03: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:03: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:03: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:03: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:03: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 07:37:03: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Apr 2021 07:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.20_model.r WARNING @ Sat, 03 Apr 2021 07:37:03: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:03: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sat, 03 Apr 2021 07:37:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:37:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.10_summits.bed INFO @ Sat, 03 Apr 2021 07:37:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3438 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029132/SRX3029132.20_summits.bed INFO @ Sat, 03 Apr 2021 07:37:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1475 records, 4 fields): 4 millis CompletedMACS2peakCalling