Job ID = 14158236 SRX = SRX10641210 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: 00:24:50 19663986 reads; of these: 19663986 (100.00%) were paired; of these: 12847080 (65.33%) aligned concordantly 0 times 5718771 (29.08%) aligned concordantly exactly 1 time 1098135 (5.58%) aligned concordantly >1 times ---- 12847080 pairs aligned concordantly 0 times; of these: 3068950 (23.89%) aligned discordantly 1 time ---- 9778130 pairs aligned 0 times concordantly or discordantly; of these: 19556260 mates make up the pairs; of these: 18062926 (92.36%) aligned 0 times 811969 (4.15%) aligned exactly 1 time 681365 (3.48%) aligned >1 times 54.07% overall alignment rate Time searching: 00:24:50 Overall time: 00:24:50 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] 1444639 / 9855847 = 0.1466 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 15:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.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 15:33:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:33:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:33:58: 1000000 INFO @ Wed, 08 Dec 2021 15:34:08: 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 15:34:18: 3000000 INFO @ Wed, 08 Dec 2021 15:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.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 15:34:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:34:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:34:28: 4000000 INFO @ Wed, 08 Dec 2021 15:34:29: 1000000 INFO @ Wed, 08 Dec 2021 15:34:39: 5000000 INFO @ Wed, 08 Dec 2021 15:34:39: 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 15:34:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.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 15:34:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:34:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:34:49: 3000000 INFO @ Wed, 08 Dec 2021 15:34:49: 6000000 INFO @ Wed, 08 Dec 2021 15:34:58: 1000000 INFO @ Wed, 08 Dec 2021 15:34:59: 4000000 INFO @ Wed, 08 Dec 2021 15:35:00: 7000000 INFO @ Wed, 08 Dec 2021 15:35:09: 2000000 INFO @ Wed, 08 Dec 2021 15:35:10: 5000000 INFO @ Wed, 08 Dec 2021 15:35:11: 8000000 INFO @ Wed, 08 Dec 2021 15:35:18: 3000000 INFO @ Wed, 08 Dec 2021 15:35:20: 6000000 INFO @ Wed, 08 Dec 2021 15:35:22: 9000000 INFO @ Wed, 08 Dec 2021 15:35:28: 4000000 INFO @ Wed, 08 Dec 2021 15:35:31: 7000000 INFO @ Wed, 08 Dec 2021 15:35:32: 10000000 INFO @ Wed, 08 Dec 2021 15:35:38: 5000000 INFO @ Wed, 08 Dec 2021 15:35:42: 8000000 INFO @ Wed, 08 Dec 2021 15:35:43: 11000000 INFO @ Wed, 08 Dec 2021 15:35:48: 6000000 INFO @ Wed, 08 Dec 2021 15:35:52: 9000000 INFO @ Wed, 08 Dec 2021 15:35:54: 12000000 INFO @ Wed, 08 Dec 2021 15:35:58: 7000000 INFO @ Wed, 08 Dec 2021 15:36:03: 10000000 INFO @ Wed, 08 Dec 2021 15:36:05: 13000000 INFO @ Wed, 08 Dec 2021 15:36:07: 8000000 INFO @ Wed, 08 Dec 2021 15:36:14: 11000000 INFO @ Wed, 08 Dec 2021 15:36:16: 14000000 INFO @ Wed, 08 Dec 2021 15:36:17: 9000000 INFO @ Wed, 08 Dec 2021 15:36:24: 12000000 INFO @ Wed, 08 Dec 2021 15:36:27: 15000000 INFO @ Wed, 08 Dec 2021 15:36:27: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:36:35: 13000000 INFO @ Wed, 08 Dec 2021 15:36:37: 11000000 INFO @ Wed, 08 Dec 2021 15:36:37: 16000000 INFO @ Wed, 08 Dec 2021 15:36:46: 14000000 INFO @ Wed, 08 Dec 2021 15:36:47: 12000000 INFO @ Wed, 08 Dec 2021 15:36:48: 17000000 INFO @ Wed, 08 Dec 2021 15:36:56: 13000000 INFO @ Wed, 08 Dec 2021 15:36:57: 15000000 INFO @ Wed, 08 Dec 2021 15:36:59: 18000000 INFO @ Wed, 08 Dec 2021 15:37:03: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:37:03: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:37:03: #1 total tags in treatment: 5735365 INFO @ Wed, 08 Dec 2021 15:37:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:37:03: #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 15:37:03: #1 tags after filtering in treatment: 5349464 INFO @ Wed, 08 Dec 2021 15:37:03: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:37:03: #1 finished! INFO @ Wed, 08 Dec 2021 15:37:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:37:04: #2 number of paired peaks: 583 WARNING @ Wed, 08 Dec 2021 15:37:04: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Wed, 08 Dec 2021 15:37:04: start model_add_line... INFO @ Wed, 08 Dec 2021 15:37:04: start X-correlation... INFO @ Wed, 08 Dec 2021 15:37:04: end of X-cor INFO @ Wed, 08 Dec 2021 15:37:04: #2 finished! INFO @ Wed, 08 Dec 2021 15:37:04: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 15:37:04: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 15:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.05_model.r WARNING @ Wed, 08 Dec 2021 15:37:04: #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 15:37:04: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 15:37:04: #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 15:37:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:37:06: 14000000 INFO @ Wed, 08 Dec 2021 15:37:08: 16000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:37:15: 15000000 INFO @ Wed, 08 Dec 2021 15:37:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:37:19: 17000000 INFO @ Wed, 08 Dec 2021 15:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.05_summits.bed INFO @ Wed, 08 Dec 2021 15:37:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:37:25: 16000000 INFO @ Wed, 08 Dec 2021 15:37:30: 18000000 INFO @ Wed, 08 Dec 2021 15:37:34: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:37:34: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:37:34: #1 total tags in treatment: 5735365 INFO @ Wed, 08 Dec 2021 15:37:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:37:34: #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 15:37:34: #1 tags after filtering in treatment: 5349464 INFO @ Wed, 08 Dec 2021 15:37:34: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:37:34: #1 finished! INFO @ Wed, 08 Dec 2021 15:37:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:37:34: #2 number of paired peaks: 583 WARNING @ Wed, 08 Dec 2021 15:37:34: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Wed, 08 Dec 2021 15:37:34: start model_add_line... INFO @ Wed, 08 Dec 2021 15:37:34: start X-correlation... INFO @ Wed, 08 Dec 2021 15:37:34: end of X-cor INFO @ Wed, 08 Dec 2021 15:37:34: #2 finished! INFO @ Wed, 08 Dec 2021 15:37:34: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 15:37:34: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 15:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.10_model.r WARNING @ Wed, 08 Dec 2021 15:37:34: #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 15:37:34: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 15:37:34: #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 15:37:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:37:35: 17000000 INFO @ Wed, 08 Dec 2021 15:37:43: 18000000 INFO @ Wed, 08 Dec 2021 15:37:46: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:37:46: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:37:46: #1 total tags in treatment: 5735365 INFO @ Wed, 08 Dec 2021 15:37:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:37:46: #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 15:37:47: #1 tags after filtering in treatment: 5349464 INFO @ Wed, 08 Dec 2021 15:37:47: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:37:47: #1 finished! INFO @ Wed, 08 Dec 2021 15:37:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:37:47: #2 number of paired peaks: 583 WARNING @ Wed, 08 Dec 2021 15:37:47: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Wed, 08 Dec 2021 15:37:47: start model_add_line... INFO @ Wed, 08 Dec 2021 15:37:47: start X-correlation... INFO @ Wed, 08 Dec 2021 15:37:47: end of X-cor INFO @ Wed, 08 Dec 2021 15:37:47: #2 finished! INFO @ Wed, 08 Dec 2021 15:37:47: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 15:37:47: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 15:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.20_model.r WARNING @ Wed, 08 Dec 2021 15:37:47: #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 15:37:47: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 15:37:47: #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 15:37:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:37:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.10_summits.bed INFO @ Wed, 08 Dec 2021 15:37:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (321 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:38:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:38:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641210/SRX10641210.20_summits.bed INFO @ Wed, 08 Dec 2021 15:38:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling