Job ID = 12265402 SRX = SRX7687155 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: 00:27:32 26612955 reads; of these: 26612955 (100.00%) were paired; of these: 4650701 (17.48%) aligned concordantly 0 times 19817253 (74.46%) aligned concordantly exactly 1 time 2145001 (8.06%) aligned concordantly >1 times ---- 4650701 pairs aligned concordantly 0 times; of these: 2629670 (56.54%) aligned discordantly 1 time ---- 2021031 pairs aligned 0 times concordantly or discordantly; of these: 4042062 mates make up the pairs; of these: 3251652 (80.45%) aligned 0 times 391544 (9.69%) aligned exactly 1 time 398866 (9.87%) aligned >1 times 93.89% overall alignment rate Time searching: 00:27:32 Overall time: 00:27:32 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 24 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] 13910887 / 24555922 = 0.5665 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 07:28:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.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 07:28:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:28:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:21: 1000000 INFO @ Sat, 03 Apr 2021 07:28:28: 2000000 INFO @ Sat, 03 Apr 2021 07:28:34: 3000000 INFO @ Sat, 03 Apr 2021 07:28:40: 4000000 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 07:28:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.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 07:28:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:28:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:46: 5000000 INFO @ Sat, 03 Apr 2021 07:28:51: 1000000 INFO @ Sat, 03 Apr 2021 07:28:53: 6000000 INFO @ Sat, 03 Apr 2021 07:28:57: 2000000 INFO @ Sat, 03 Apr 2021 07:28:59: 7000000 INFO @ Sat, 03 Apr 2021 07:29:02: 3000000 INFO @ Sat, 03 Apr 2021 07:29:06: 8000000 INFO @ Sat, 03 Apr 2021 07:29:08: 4000000 INFO @ Sat, 03 Apr 2021 07:29:12: 9000000 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 07:29:14: 5000000 INFO @ Sat, 03 Apr 2021 07:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.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 07:29:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:29:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:29:19: 10000000 INFO @ Sat, 03 Apr 2021 07:29:20: 6000000 INFO @ Sat, 03 Apr 2021 07:29:21: 1000000 INFO @ Sat, 03 Apr 2021 07:29:25: 11000000 INFO @ Sat, 03 Apr 2021 07:29:26: 7000000 INFO @ Sat, 03 Apr 2021 07:29:27: 2000000 INFO @ Sat, 03 Apr 2021 07:29:32: 12000000 INFO @ Sat, 03 Apr 2021 07:29:32: 8000000 INFO @ Sat, 03 Apr 2021 07:29:33: 3000000 INFO @ Sat, 03 Apr 2021 07:29:38: 9000000 INFO @ Sat, 03 Apr 2021 07:29:38: 13000000 INFO @ Sat, 03 Apr 2021 07:29:39: 4000000 INFO @ Sat, 03 Apr 2021 07:29:44: 10000000 INFO @ Sat, 03 Apr 2021 07:29:45: 5000000 INFO @ Sat, 03 Apr 2021 07:29:45: 14000000 INFO @ Sat, 03 Apr 2021 07:29:50: 11000000 INFO @ Sat, 03 Apr 2021 07:29:51: 6000000 INFO @ Sat, 03 Apr 2021 07:29:52: 15000000 INFO @ Sat, 03 Apr 2021 07:29:56: 12000000 INFO @ Sat, 03 Apr 2021 07:29:57: 7000000 INFO @ Sat, 03 Apr 2021 07:29:58: 16000000 INFO @ Sat, 03 Apr 2021 07:30:02: 13000000 INFO @ Sat, 03 Apr 2021 07:30:03: 8000000 INFO @ Sat, 03 Apr 2021 07:30:05: 17000000 INFO @ Sat, 03 Apr 2021 07:30:08: 14000000 INFO @ Sat, 03 Apr 2021 07:30:08: 9000000 INFO @ Sat, 03 Apr 2021 07:30:12: 18000000 INFO @ Sat, 03 Apr 2021 07:30:13: 15000000 INFO @ Sat, 03 Apr 2021 07:30:14: 10000000 INFO @ Sat, 03 Apr 2021 07:30:18: 19000000 INFO @ Sat, 03 Apr 2021 07:30:19: 16000000 INFO @ Sat, 03 Apr 2021 07:30:20: 11000000 INFO @ Sat, 03 Apr 2021 07:30:24: 20000000 INFO @ Sat, 03 Apr 2021 07:30:25: 17000000 INFO @ Sat, 03 Apr 2021 07:30:26: 12000000 INFO @ Sat, 03 Apr 2021 07:30:30: 21000000 INFO @ Sat, 03 Apr 2021 07:30:31: 18000000 INFO @ Sat, 03 Apr 2021 07:30:32: 13000000 INFO @ Sat, 03 Apr 2021 07:30:36: 19000000 INFO @ Sat, 03 Apr 2021 07:30:36: 22000000 INFO @ Sat, 03 Apr 2021 07:30:37: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:30:37: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:30:37: #1 total tags in treatment: 9379528 INFO @ Sat, 03 Apr 2021 07:30:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:30:37: #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 07:30:38: #1 tags after filtering in treatment: 7067848 INFO @ Sat, 03 Apr 2021 07:30:38: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:30:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:30:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:30:38: 14000000 INFO @ Sat, 03 Apr 2021 07:30:38: #2 number of paired peaks: 355 WARNING @ Sat, 03 Apr 2021 07:30:38: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Sat, 03 Apr 2021 07:30:38: start model_add_line... INFO @ Sat, 03 Apr 2021 07:30:38: start X-correlation... INFO @ Sat, 03 Apr 2021 07:30:38: end of X-cor INFO @ Sat, 03 Apr 2021 07:30:38: #2 finished! INFO @ Sat, 03 Apr 2021 07:30:38: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:30:38: #2 alternative fragment length(s) may be 4,123,141,153,181 bps INFO @ Sat, 03 Apr 2021 07:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.05_model.r WARNING @ Sat, 03 Apr 2021 07:30:38: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:30:38: #2 You may need to consider one of the other alternative d(s): 4,123,141,153,181 WARNING @ Sat, 03 Apr 2021 07:30:38: #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 07:30:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:30:42: 20000000 INFO @ Sat, 03 Apr 2021 07:30:43: 15000000 INFO @ Sat, 03 Apr 2021 07:30:47: 21000000 INFO @ Sat, 03 Apr 2021 07:30:49: 16000000 INFO @ Sat, 03 Apr 2021 07:30:52: 22000000 INFO @ Sat, 03 Apr 2021 07:30:53: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:30:53: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:30:53: #1 total tags in treatment: 9379528 INFO @ Sat, 03 Apr 2021 07:30:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:30:53: #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 07:30:53: #1 tags after filtering in treatment: 7067848 INFO @ Sat, 03 Apr 2021 07:30:53: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:30:53: #1 finished! INFO @ Sat, 03 Apr 2021 07:30:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:30:54: #2 number of paired peaks: 355 WARNING @ Sat, 03 Apr 2021 07:30:54: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Sat, 03 Apr 2021 07:30:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:30:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:30:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:30:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:30:54: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:30:54: #2 alternative fragment length(s) may be 4,123,141,153,181 bps INFO @ Sat, 03 Apr 2021 07:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.10_model.r WARNING @ Sat, 03 Apr 2021 07:30:54: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:30:54: #2 You may need to consider one of the other alternative d(s): 4,123,141,153,181 WARNING @ Sat, 03 Apr 2021 07:30:54: #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 07:30:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:30:55: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:30:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:31:00: 18000000 INFO @ Sat, 03 Apr 2021 07:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.05_summits.bed INFO @ Sat, 03 Apr 2021 07:31:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (796 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:31:06: 19000000 INFO @ Sat, 03 Apr 2021 07:31:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:31:11: 20000000 INFO @ Sat, 03 Apr 2021 07:31:16: 21000000 INFO @ Sat, 03 Apr 2021 07:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.10_summits.bed INFO @ Sat, 03 Apr 2021 07:31:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:31:21: 22000000 INFO @ Sat, 03 Apr 2021 07:31:22: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:31:22: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:31:22: #1 total tags in treatment: 9379528 INFO @ Sat, 03 Apr 2021 07:31:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:31:22: #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 07:31:22: #1 tags after filtering in treatment: 7067848 INFO @ Sat, 03 Apr 2021 07:31:22: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:31:22: #1 finished! INFO @ Sat, 03 Apr 2021 07:31:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:31:23: #2 number of paired peaks: 355 WARNING @ Sat, 03 Apr 2021 07:31:23: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Sat, 03 Apr 2021 07:31:23: start model_add_line... INFO @ Sat, 03 Apr 2021 07:31:23: start X-correlation... INFO @ Sat, 03 Apr 2021 07:31:23: end of X-cor INFO @ Sat, 03 Apr 2021 07:31:23: #2 finished! INFO @ Sat, 03 Apr 2021 07:31:23: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:31:23: #2 alternative fragment length(s) may be 4,123,141,153,181 bps INFO @ Sat, 03 Apr 2021 07:31:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.20_model.r WARNING @ Sat, 03 Apr 2021 07:31:23: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:31:23: #2 You may need to consider one of the other alternative d(s): 4,123,141,153,181 WARNING @ Sat, 03 Apr 2021 07:31:23: #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 07:31:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:31:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:31:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687155/SRX7687155.20_summits.bed INFO @ Sat, 03 Apr 2021 07:31:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 1 millis CompletedMACS2peakCalling