Job ID = 16434986 SRX = SRX13336898 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 16467884 reads; of these: 16467884 (100.00%) were paired; of these: 7956590 (48.32%) aligned concordantly 0 times 7212000 (43.79%) aligned concordantly exactly 1 time 1299294 (7.89%) aligned concordantly >1 times ---- 7956590 pairs aligned concordantly 0 times; of these: 3349597 (42.10%) aligned discordantly 1 time ---- 4606993 pairs aligned 0 times concordantly or discordantly; of these: 9213986 mates make up the pairs; of these: 7917309 (85.93%) aligned 0 times 626737 (6.80%) aligned exactly 1 time 669940 (7.27%) aligned >1 times 75.96% 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] 1090450 / 11820906 = 0.0922 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.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 @ Tue, 02 Aug 2022 11:05:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:05:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:00: 1000000 INFO @ Tue, 02 Aug 2022 11:06:10: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.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 @ Tue, 02 Aug 2022 11:06:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:20: 3000000 INFO @ Tue, 02 Aug 2022 11:06:30: 1000000 INFO @ Tue, 02 Aug 2022 11:06:31: 4000000 INFO @ Tue, 02 Aug 2022 11:06:41: 2000000 INFO @ Tue, 02 Aug 2022 11:06:41: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.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 @ Tue, 02 Aug 2022 11:06:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:51: 3000000 INFO @ Tue, 02 Aug 2022 11:06:52: 6000000 INFO @ Tue, 02 Aug 2022 11:07:00: 1000000 INFO @ Tue, 02 Aug 2022 11:07:02: 4000000 INFO @ Tue, 02 Aug 2022 11:07:02: 7000000 INFO @ Tue, 02 Aug 2022 11:07:09: 2000000 INFO @ Tue, 02 Aug 2022 11:07:13: 5000000 INFO @ Tue, 02 Aug 2022 11:07:13: 8000000 INFO @ Tue, 02 Aug 2022 11:07:19: 3000000 INFO @ Tue, 02 Aug 2022 11:07:24: 6000000 INFO @ Tue, 02 Aug 2022 11:07:24: 9000000 INFO @ Tue, 02 Aug 2022 11:07:29: 4000000 INFO @ Tue, 02 Aug 2022 11:07:34: 7000000 INFO @ Tue, 02 Aug 2022 11:07:35: 10000000 INFO @ Tue, 02 Aug 2022 11:07:40: 5000000 INFO @ Tue, 02 Aug 2022 11:07:45: 8000000 INFO @ Tue, 02 Aug 2022 11:07:46: 11000000 INFO @ Tue, 02 Aug 2022 11:07:50: 6000000 INFO @ Tue, 02 Aug 2022 11:07:56: 9000000 INFO @ Tue, 02 Aug 2022 11:07:56: 12000000 INFO @ Tue, 02 Aug 2022 11:08:00: 7000000 INFO @ Tue, 02 Aug 2022 11:08:07: 10000000 INFO @ Tue, 02 Aug 2022 11:08:07: 13000000 INFO @ Tue, 02 Aug 2022 11:08:10: 8000000 INFO @ Tue, 02 Aug 2022 11:08:16: 14000000 INFO @ Tue, 02 Aug 2022 11:08:17: 11000000 INFO @ Tue, 02 Aug 2022 11:08:20: 9000000 INFO @ Tue, 02 Aug 2022 11:08:26: 15000000 INFO @ Tue, 02 Aug 2022 11:08:28: 12000000 INFO @ Tue, 02 Aug 2022 11:08:30: 10000000 INFO @ Tue, 02 Aug 2022 11:08:36: 16000000 INFO @ Tue, 02 Aug 2022 11:08:39: 13000000 INFO @ Tue, 02 Aug 2022 11:08:40: 11000000 INFO @ Tue, 02 Aug 2022 11:08:46: 17000000 INFO @ Tue, 02 Aug 2022 11:08:49: 14000000 INFO @ Tue, 02 Aug 2022 11:08:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:08:57: 18000000 INFO @ Tue, 02 Aug 2022 11:09:00: 13000000 INFO @ Tue, 02 Aug 2022 11:09:00: 15000000 INFO @ Tue, 02 Aug 2022 11:09:08: 19000000 INFO @ Tue, 02 Aug 2022 11:09:09: 14000000 INFO @ Tue, 02 Aug 2022 11:09:11: 16000000 INFO @ Tue, 02 Aug 2022 11:09:19: 20000000 INFO @ Tue, 02 Aug 2022 11:09:19: 15000000 INFO @ Tue, 02 Aug 2022 11:09:21: 17000000 INFO @ Tue, 02 Aug 2022 11:09:29: 16000000 INFO @ Tue, 02 Aug 2022 11:09:30: 21000000 INFO @ Tue, 02 Aug 2022 11:09:32: 18000000 INFO @ Tue, 02 Aug 2022 11:09:38: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:09:40: 22000000 INFO @ Tue, 02 Aug 2022 11:09:43: 19000000 INFO @ Tue, 02 Aug 2022 11:09:48: 18000000 INFO @ Tue, 02 Aug 2022 11:09:49: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:09:49: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:09:49: #1 total tags in treatment: 7657408 INFO @ Tue, 02 Aug 2022 11:09:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:09:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:09:49: #1 tags after filtering in treatment: 7080573 INFO @ Tue, 02 Aug 2022 11:09:49: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:09:49: #1 finished! INFO @ Tue, 02 Aug 2022 11:09:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:09:50: #2 number of paired peaks: 534 WARNING @ Tue, 02 Aug 2022 11:09:50: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Tue, 02 Aug 2022 11:09:50: start model_add_line... INFO @ Tue, 02 Aug 2022 11:09:50: start X-correlation... INFO @ Tue, 02 Aug 2022 11:09:50: end of X-cor INFO @ Tue, 02 Aug 2022 11:09:50: #2 finished! INFO @ Tue, 02 Aug 2022 11:09:50: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:09:50: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.05_model.r WARNING @ Tue, 02 Aug 2022 11:09:50: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:09:50: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:09:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:09:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:09:53: 20000000 INFO @ Tue, 02 Aug 2022 11:09:59: 19000000 INFO @ Tue, 02 Aug 2022 11:10:02: 21000000 INFO @ Tue, 02 Aug 2022 11:10:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:10:09: 20000000 INFO @ Tue, 02 Aug 2022 11:10:12: 22000000 INFO @ Tue, 02 Aug 2022 11:10:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:10:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:10:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.05_summits.bed INFO @ Tue, 02 Aug 2022 11:10:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:10:19: 21000000 INFO @ Tue, 02 Aug 2022 11:10:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:10:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:10:21: #1 total tags in treatment: 7657408 INFO @ Tue, 02 Aug 2022 11:10:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:10:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:10:21: #1 tags after filtering in treatment: 7080573 INFO @ Tue, 02 Aug 2022 11:10:21: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:10:21: #1 finished! INFO @ Tue, 02 Aug 2022 11:10:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:10:21: #2 number of paired peaks: 534 WARNING @ Tue, 02 Aug 2022 11:10:21: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Tue, 02 Aug 2022 11:10:21: start model_add_line... INFO @ Tue, 02 Aug 2022 11:10:21: start X-correlation... INFO @ Tue, 02 Aug 2022 11:10:21: end of X-cor INFO @ Tue, 02 Aug 2022 11:10:21: #2 finished! INFO @ Tue, 02 Aug 2022 11:10:21: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:10:21: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.10_model.r WARNING @ Tue, 02 Aug 2022 11:10:21: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:10:21: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:10:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:10:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:10:29: 22000000 INFO @ Tue, 02 Aug 2022 11:10:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:10:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:10:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:10:37: #1 total tags in treatment: 7657408 INFO @ Tue, 02 Aug 2022 11:10:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:10:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:10:37: #1 tags after filtering in treatment: 7080573 INFO @ Tue, 02 Aug 2022 11:10:37: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:10:37: #1 finished! INFO @ Tue, 02 Aug 2022 11:10:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:10:38: #2 number of paired peaks: 534 WARNING @ Tue, 02 Aug 2022 11:10:38: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Tue, 02 Aug 2022 11:10:38: start model_add_line... INFO @ Tue, 02 Aug 2022 11:10:38: start X-correlation... INFO @ Tue, 02 Aug 2022 11:10:38: end of X-cor INFO @ Tue, 02 Aug 2022 11:10:38: #2 finished! INFO @ Tue, 02 Aug 2022 11:10:38: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:10:38: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.20_model.r WARNING @ Tue, 02 Aug 2022 11:10:38: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:10:38: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:10:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:10:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.10_summits.bed INFO @ Tue, 02 Aug 2022 11:10:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 137 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:10:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336898/SRX13336898.20_summits.bed INFO @ Tue, 02 Aug 2022 11:11:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 28 millis CompletedMACS2peakCalling