Job ID = 14158408 SRX = SRX10641218 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: 00:25:09 17078397 reads; of these: 17078397 (100.00%) were paired; of these: 9620853 (56.33%) aligned concordantly 0 times 6247136 (36.58%) aligned concordantly exactly 1 time 1210408 (7.09%) aligned concordantly >1 times ---- 9620853 pairs aligned concordantly 0 times; of these: 2825627 (29.37%) aligned discordantly 1 time ---- 6795226 pairs aligned 0 times concordantly or discordantly; of these: 13590452 mates make up the pairs; of these: 12293172 (90.45%) aligned 0 times 660859 (4.86%) aligned exactly 1 time 636421 (4.68%) aligned >1 times 64.01% overall alignment rate Time searching: 00:25:09 Overall time: 00:25:09 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] 1254657 / 10253357 = 0.1224 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 18:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.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 18:05:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:05:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:05:25: 1000000 INFO @ Wed, 08 Dec 2021 18:05:36: 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 18:05:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.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 18:05:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:05:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:05:47: 3000000 INFO @ Wed, 08 Dec 2021 18:05:56: 1000000 INFO @ Wed, 08 Dec 2021 18:06:00: 4000000 INFO @ Wed, 08 Dec 2021 18:06:09: 2000000 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 18:06:12: 5000000 INFO @ Wed, 08 Dec 2021 18:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.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 18:06:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:06:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:06:22: 3000000 INFO @ Wed, 08 Dec 2021 18:06:25: 6000000 INFO @ Wed, 08 Dec 2021 18:06:25: 1000000 INFO @ Wed, 08 Dec 2021 18:06:35: 4000000 INFO @ Wed, 08 Dec 2021 18:06:36: 2000000 INFO @ Wed, 08 Dec 2021 18:06:37: 7000000 INFO @ Wed, 08 Dec 2021 18:06:47: 3000000 INFO @ Wed, 08 Dec 2021 18:06:48: 5000000 INFO @ Wed, 08 Dec 2021 18:06:50: 8000000 INFO @ Wed, 08 Dec 2021 18:06:58: 4000000 INFO @ Wed, 08 Dec 2021 18:07:01: 6000000 INFO @ Wed, 08 Dec 2021 18:07:03: 9000000 INFO @ Wed, 08 Dec 2021 18:07:09: 5000000 INFO @ Wed, 08 Dec 2021 18:07:14: 7000000 INFO @ Wed, 08 Dec 2021 18:07:15: 10000000 INFO @ Wed, 08 Dec 2021 18:07:19: 6000000 INFO @ Wed, 08 Dec 2021 18:07:26: 8000000 INFO @ Wed, 08 Dec 2021 18:07:28: 11000000 INFO @ Wed, 08 Dec 2021 18:07:31: 7000000 INFO @ Wed, 08 Dec 2021 18:07:39: 9000000 INFO @ Wed, 08 Dec 2021 18:07:41: 12000000 INFO @ Wed, 08 Dec 2021 18:07:42: 8000000 INFO @ Wed, 08 Dec 2021 18:07:52: 10000000 INFO @ Wed, 08 Dec 2021 18:07:53: 9000000 INFO @ Wed, 08 Dec 2021 18:07:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:08:04: 10000000 INFO @ Wed, 08 Dec 2021 18:08:05: 11000000 INFO @ Wed, 08 Dec 2021 18:08:06: 14000000 INFO @ Wed, 08 Dec 2021 18:08:15: 11000000 INFO @ Wed, 08 Dec 2021 18:08:18: 12000000 INFO @ Wed, 08 Dec 2021 18:08:19: 15000000 INFO @ Wed, 08 Dec 2021 18:08:26: 12000000 INFO @ Wed, 08 Dec 2021 18:08:31: 16000000 INFO @ Wed, 08 Dec 2021 18:08:31: 13000000 INFO @ Wed, 08 Dec 2021 18:08:38: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:08:43: 17000000 INFO @ Wed, 08 Dec 2021 18:08:44: 14000000 INFO @ Wed, 08 Dec 2021 18:08:49: 14000000 INFO @ Wed, 08 Dec 2021 18:08:56: 18000000 INFO @ Wed, 08 Dec 2021 18:08:57: 15000000 INFO @ Wed, 08 Dec 2021 18:09:00: 15000000 INFO @ Wed, 08 Dec 2021 18:09:08: 19000000 INFO @ Wed, 08 Dec 2021 18:09:10: 16000000 INFO @ Wed, 08 Dec 2021 18:09:12: 16000000 INFO @ Wed, 08 Dec 2021 18:09:13: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:09:13: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:09:13: #1 total tags in treatment: 6467594 INFO @ Wed, 08 Dec 2021 18:09:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:09:13: #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 18:09:13: #1 tags after filtering in treatment: 5936990 INFO @ Wed, 08 Dec 2021 18:09:13: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:09:13: #1 finished! INFO @ Wed, 08 Dec 2021 18:09:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:09:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:09:13: #2 number of paired peaks: 599 WARNING @ Wed, 08 Dec 2021 18:09:13: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Wed, 08 Dec 2021 18:09:13: start model_add_line... INFO @ Wed, 08 Dec 2021 18:09:13: start X-correlation... INFO @ Wed, 08 Dec 2021 18:09:13: end of X-cor INFO @ Wed, 08 Dec 2021 18:09:13: #2 finished! INFO @ Wed, 08 Dec 2021 18:09:13: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 18:09:13: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 18:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.05_model.r WARNING @ Wed, 08 Dec 2021 18:09:14: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:09:14: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 18:09:14: #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 18:09:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:09:22: 17000000 INFO @ Wed, 08 Dec 2021 18:09:23: 17000000 INFO @ Wed, 08 Dec 2021 18:09:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.05_summits.bed INFO @ Wed, 08 Dec 2021 18:09:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:09:35: 18000000 INFO @ Wed, 08 Dec 2021 18:09:36: 18000000 INFO @ Wed, 08 Dec 2021 18:09:48: 19000000 INFO @ Wed, 08 Dec 2021 18:09:49: 19000000 INFO @ Wed, 08 Dec 2021 18:09:53: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:09:53: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:09:53: #1 total tags in treatment: 6467594 INFO @ Wed, 08 Dec 2021 18:09:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:09:53: #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 18:09:53: #1 tags after filtering in treatment: 5936990 INFO @ Wed, 08 Dec 2021 18:09:53: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:09:53: #1 finished! INFO @ Wed, 08 Dec 2021 18:09:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:09:53: #2 number of paired peaks: 599 WARNING @ Wed, 08 Dec 2021 18:09:53: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Wed, 08 Dec 2021 18:09:53: start model_add_line... INFO @ Wed, 08 Dec 2021 18:09:53: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:09:53: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:09:53: #1 total tags in treatment: 6467594 INFO @ Wed, 08 Dec 2021 18:09:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:09:53: #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 18:09:53: start X-correlation... INFO @ Wed, 08 Dec 2021 18:09:53: end of X-cor INFO @ Wed, 08 Dec 2021 18:09:53: #2 finished! INFO @ Wed, 08 Dec 2021 18:09:53: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 18:09:53: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 18:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.10_model.r WARNING @ Wed, 08 Dec 2021 18:09:53: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:09:53: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 18:09:53: #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 18:09:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:09:53: #1 tags after filtering in treatment: 5936990 INFO @ Wed, 08 Dec 2021 18:09:53: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:09:53: #1 finished! INFO @ Wed, 08 Dec 2021 18:09:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:09:54: #2 number of paired peaks: 599 WARNING @ Wed, 08 Dec 2021 18:09:54: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Wed, 08 Dec 2021 18:09:54: start model_add_line... INFO @ Wed, 08 Dec 2021 18:09:54: start X-correlation... INFO @ Wed, 08 Dec 2021 18:09:54: end of X-cor INFO @ Wed, 08 Dec 2021 18:09:54: #2 finished! INFO @ Wed, 08 Dec 2021 18:09:54: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 18:09:54: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 18:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.20_model.r WARNING @ Wed, 08 Dec 2021 18:09:54: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:09:54: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 18:09:54: #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 18:09:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:10:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:10:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:10:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:10:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:10:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.10_summits.bed INFO @ Wed, 08 Dec 2021 18:10:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (378 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641218/SRX10641218.20_summits.bed INFO @ Wed, 08 Dec 2021 18:10:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling