Job ID = 14159170 SRX = SRX10641197 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: 00:26:11 15821510 reads; of these: 15821510 (100.00%) were paired; of these: 6460342 (40.83%) aligned concordantly 0 times 7934270 (50.15%) aligned concordantly exactly 1 time 1426898 (9.02%) aligned concordantly >1 times ---- 6460342 pairs aligned concordantly 0 times; of these: 2077385 (32.16%) aligned discordantly 1 time ---- 4382957 pairs aligned 0 times concordantly or discordantly; of these: 8765914 mates make up the pairs; of these: 7891303 (90.02%) aligned 0 times 434374 (4.96%) aligned exactly 1 time 440237 (5.02%) aligned >1 times 75.06% overall alignment rate Time searching: 00:26:11 Overall time: 00:26:11 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] 1391840 / 11394951 = 0.1221 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 20:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.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 20:42:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:42:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:42:29: 1000000 INFO @ Wed, 08 Dec 2021 20:42:37: 2000000 INFO @ Wed, 08 Dec 2021 20:42:45: 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 20:42:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.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 20:42:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:42:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:42:53: 4000000 INFO @ Wed, 08 Dec 2021 20:43:00: 1000000 INFO @ Wed, 08 Dec 2021 20:43:03: 5000000 INFO @ Wed, 08 Dec 2021 20:43:10: 2000000 INFO @ Wed, 08 Dec 2021 20:43:13: 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 20:43:19: 3000000 INFO @ Wed, 08 Dec 2021 20:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.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 20:43:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:43:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:43:23: 7000000 INFO @ Wed, 08 Dec 2021 20:43:30: 4000000 INFO @ Wed, 08 Dec 2021 20:43:30: 1000000 INFO @ Wed, 08 Dec 2021 20:43:33: 8000000 INFO @ Wed, 08 Dec 2021 20:43:40: 5000000 INFO @ Wed, 08 Dec 2021 20:43:40: 2000000 INFO @ Wed, 08 Dec 2021 20:43:43: 9000000 INFO @ Wed, 08 Dec 2021 20:43:50: 6000000 INFO @ Wed, 08 Dec 2021 20:43:50: 3000000 INFO @ Wed, 08 Dec 2021 20:43:53: 10000000 INFO @ Wed, 08 Dec 2021 20:44:00: 7000000 INFO @ Wed, 08 Dec 2021 20:44:00: 4000000 INFO @ Wed, 08 Dec 2021 20:44:03: 11000000 INFO @ Wed, 08 Dec 2021 20:44:10: 8000000 INFO @ Wed, 08 Dec 2021 20:44:10: 5000000 INFO @ Wed, 08 Dec 2021 20:44:13: 12000000 INFO @ Wed, 08 Dec 2021 20:44:20: 9000000 INFO @ Wed, 08 Dec 2021 20:44:20: 6000000 INFO @ Wed, 08 Dec 2021 20:44:23: 13000000 INFO @ Wed, 08 Dec 2021 20:44:30: 10000000 INFO @ Wed, 08 Dec 2021 20:44:30: 7000000 INFO @ Wed, 08 Dec 2021 20:44:33: 14000000 INFO @ Wed, 08 Dec 2021 20:44:40: 11000000 INFO @ Wed, 08 Dec 2021 20:44:40: 8000000 INFO @ Wed, 08 Dec 2021 20:44:43: 15000000 INFO @ Wed, 08 Dec 2021 20:44:50: 12000000 INFO @ Wed, 08 Dec 2021 20:44:50: 9000000 INFO @ Wed, 08 Dec 2021 20:44:53: 16000000 INFO @ Wed, 08 Dec 2021 20:45:00: 13000000 INFO @ Wed, 08 Dec 2021 20:45:00: 10000000 INFO @ Wed, 08 Dec 2021 20:45:03: 17000000 INFO @ Wed, 08 Dec 2021 20:45:10: 14000000 INFO @ Wed, 08 Dec 2021 20:45:10: 11000000 INFO @ Wed, 08 Dec 2021 20:45:13: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:45:20: 15000000 INFO @ Wed, 08 Dec 2021 20:45:21: 12000000 INFO @ Wed, 08 Dec 2021 20:45:23: 19000000 INFO @ Wed, 08 Dec 2021 20:45:30: 16000000 INFO @ Wed, 08 Dec 2021 20:45:31: 13000000 INFO @ Wed, 08 Dec 2021 20:45:33: 20000000 INFO @ Wed, 08 Dec 2021 20:45:41: 17000000 INFO @ Wed, 08 Dec 2021 20:45:41: 14000000 INFO @ Wed, 08 Dec 2021 20:45:43: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:45:43: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:45:43: #1 total tags in treatment: 8164941 INFO @ Wed, 08 Dec 2021 20:45:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:45:43: #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 20:45:43: #1 tags after filtering in treatment: 7620839 INFO @ Wed, 08 Dec 2021 20:45:43: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:45:43: #1 finished! INFO @ Wed, 08 Dec 2021 20:45:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:45:44: #2 number of paired peaks: 487 WARNING @ Wed, 08 Dec 2021 20:45:44: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Wed, 08 Dec 2021 20:45:44: start model_add_line... INFO @ Wed, 08 Dec 2021 20:45:44: start X-correlation... INFO @ Wed, 08 Dec 2021 20:45:44: end of X-cor INFO @ Wed, 08 Dec 2021 20:45:44: #2 finished! INFO @ Wed, 08 Dec 2021 20:45:44: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 20:45:44: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 20:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.05_model.r WARNING @ Wed, 08 Dec 2021 20:45:44: #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 20:45:44: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 20:45:44: #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 20:45:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:45:51: 18000000 INFO @ Wed, 08 Dec 2021 20:45:51: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:46:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:46:01: 19000000 INFO @ Wed, 08 Dec 2021 20:46:01: 16000000 INFO @ Wed, 08 Dec 2021 20:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.05_summits.bed INFO @ Wed, 08 Dec 2021 20:46:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:46:11: 20000000 INFO @ Wed, 08 Dec 2021 20:46:11: 17000000 INFO @ Wed, 08 Dec 2021 20:46:20: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:46:20: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:46:20: #1 total tags in treatment: 8164941 INFO @ Wed, 08 Dec 2021 20:46:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:46:20: #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 20:46:20: #1 tags after filtering in treatment: 7620839 INFO @ Wed, 08 Dec 2021 20:46:20: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:46:20: #1 finished! INFO @ Wed, 08 Dec 2021 20:46:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:46:21: #2 number of paired peaks: 487 WARNING @ Wed, 08 Dec 2021 20:46:21: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Wed, 08 Dec 2021 20:46:21: start model_add_line... INFO @ Wed, 08 Dec 2021 20:46:21: start X-correlation... INFO @ Wed, 08 Dec 2021 20:46:21: end of X-cor INFO @ Wed, 08 Dec 2021 20:46:21: #2 finished! INFO @ Wed, 08 Dec 2021 20:46:21: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 20:46:21: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 20:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.10_model.r WARNING @ Wed, 08 Dec 2021 20:46:21: #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 20:46:21: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 20:46:21: #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 20:46:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:46:21: 18000000 INFO @ Wed, 08 Dec 2021 20:46:30: 19000000 INFO @ Wed, 08 Dec 2021 20:46:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:46:39: 20000000 INFO @ Wed, 08 Dec 2021 20:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.10_summits.bed INFO @ Wed, 08 Dec 2021 20:46:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:46:48: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:46:48: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:46:48: #1 total tags in treatment: 8164941 INFO @ Wed, 08 Dec 2021 20:46:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:46:48: #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 20:46:48: #1 tags after filtering in treatment: 7620839 INFO @ Wed, 08 Dec 2021 20:46:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:46:48: #1 finished! INFO @ Wed, 08 Dec 2021 20:46:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:46:49: #2 number of paired peaks: 487 WARNING @ Wed, 08 Dec 2021 20:46:49: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Wed, 08 Dec 2021 20:46:49: start model_add_line... INFO @ Wed, 08 Dec 2021 20:46:49: start X-correlation... INFO @ Wed, 08 Dec 2021 20:46:49: end of X-cor INFO @ Wed, 08 Dec 2021 20:46:49: #2 finished! INFO @ Wed, 08 Dec 2021 20:46:49: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 20:46:49: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 20:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.20_model.r WARNING @ Wed, 08 Dec 2021 20:46:49: #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 20:46:49: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 20:46:49: #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 20:46:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:47:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641197/SRX10641197.20_summits.bed INFO @ Wed, 08 Dec 2021 20:47:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 3 millis CompletedMACS2peakCalling