Job ID = 12265403 SRX = SRX3029123 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: 00:28:18 29483489 reads; of these: 29483489 (100.00%) were paired; of these: 9136547 (30.99%) aligned concordantly 0 times 17992596 (61.03%) aligned concordantly exactly 1 time 2354346 (7.99%) aligned concordantly >1 times ---- 9136547 pairs aligned concordantly 0 times; of these: 2458171 (26.90%) aligned discordantly 1 time ---- 6678376 pairs aligned 0 times concordantly or discordantly; of these: 13356752 mates make up the pairs; of these: 12129674 (90.81%) aligned 0 times 582325 (4.36%) aligned exactly 1 time 644753 (4.83%) aligned >1 times 79.43% overall alignment rate Time searching: 00:28:18 Overall time: 00:28:18 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] 8302239 / 22613669 = 0.3671 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 07:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.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 07:36:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:36:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:36:33: 1000000 INFO @ Sat, 03 Apr 2021 07:36:39: 2000000 INFO @ Sat, 03 Apr 2021 07:36:46: 3000000 INFO @ Sat, 03 Apr 2021 07:36:53: 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 07:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.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 07:36:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:36:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:37:01: 5000000 INFO @ Sat, 03 Apr 2021 07:37:05: 1000000 INFO @ Sat, 03 Apr 2021 07:37:09: 6000000 INFO @ Sat, 03 Apr 2021 07:37:14: 2000000 INFO @ Sat, 03 Apr 2021 07:37:18: 7000000 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 07:37:23: 3000000 INFO @ Sat, 03 Apr 2021 07:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.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 07:37:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:37:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:37:26: 8000000 INFO @ Sat, 03 Apr 2021 07:37:33: 4000000 INFO @ Sat, 03 Apr 2021 07:37:34: 1000000 INFO @ Sat, 03 Apr 2021 07:37:35: 9000000 INFO @ Sat, 03 Apr 2021 07:37:42: 5000000 INFO @ Sat, 03 Apr 2021 07:37:43: 2000000 INFO @ Sat, 03 Apr 2021 07:37:44: 10000000 INFO @ Sat, 03 Apr 2021 07:37:52: 3000000 INFO @ Sat, 03 Apr 2021 07:37:52: 6000000 INFO @ Sat, 03 Apr 2021 07:37:53: 11000000 INFO @ Sat, 03 Apr 2021 07:38:00: 4000000 INFO @ Sat, 03 Apr 2021 07:38:01: 7000000 INFO @ Sat, 03 Apr 2021 07:38:02: 12000000 INFO @ Sat, 03 Apr 2021 07:38:09: 5000000 INFO @ Sat, 03 Apr 2021 07:38:10: 13000000 INFO @ Sat, 03 Apr 2021 07:38:11: 8000000 INFO @ Sat, 03 Apr 2021 07:38:18: 6000000 INFO @ Sat, 03 Apr 2021 07:38:19: 14000000 INFO @ Sat, 03 Apr 2021 07:38:20: 9000000 INFO @ Sat, 03 Apr 2021 07:38:26: 7000000 INFO @ Sat, 03 Apr 2021 07:38:28: 15000000 INFO @ Sat, 03 Apr 2021 07:38:30: 10000000 INFO @ Sat, 03 Apr 2021 07:38:35: 8000000 INFO @ Sat, 03 Apr 2021 07:38:37: 16000000 INFO @ Sat, 03 Apr 2021 07:38:39: 11000000 INFO @ Sat, 03 Apr 2021 07:38:43: 9000000 INFO @ Sat, 03 Apr 2021 07:38:46: 17000000 INFO @ Sat, 03 Apr 2021 07:38:49: 12000000 INFO @ Sat, 03 Apr 2021 07:38:52: 10000000 INFO @ Sat, 03 Apr 2021 07:38:54: 18000000 INFO @ Sat, 03 Apr 2021 07:38:58: 13000000 INFO @ Sat, 03 Apr 2021 07:39:01: 11000000 INFO @ Sat, 03 Apr 2021 07:39:03: 19000000 INFO @ Sat, 03 Apr 2021 07:39:08: 14000000 INFO @ Sat, 03 Apr 2021 07:39:10: 12000000 INFO @ Sat, 03 Apr 2021 07:39:12: 20000000 INFO @ Sat, 03 Apr 2021 07:39:17: 15000000 INFO @ Sat, 03 Apr 2021 07:39:19: 13000000 INFO @ Sat, 03 Apr 2021 07:39:21: 21000000 INFO @ Sat, 03 Apr 2021 07:39:27: 16000000 INFO @ Sat, 03 Apr 2021 07:39:27: 14000000 INFO @ Sat, 03 Apr 2021 07:39:30: 22000000 INFO @ Sat, 03 Apr 2021 07:39:36: 17000000 INFO @ Sat, 03 Apr 2021 07:39:36: 15000000 INFO @ Sat, 03 Apr 2021 07:39:39: 23000000 INFO @ Sat, 03 Apr 2021 07:39:45: 16000000 INFO @ Sat, 03 Apr 2021 07:39:46: 18000000 INFO @ Sat, 03 Apr 2021 07:39:48: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:39:54: 17000000 INFO @ Sat, 03 Apr 2021 07:39:55: 19000000 INFO @ Sat, 03 Apr 2021 07:39:56: 25000000 INFO @ Sat, 03 Apr 2021 07:40:03: 18000000 INFO @ Sat, 03 Apr 2021 07:40:04: 20000000 INFO @ Sat, 03 Apr 2021 07:40:05: 26000000 INFO @ Sat, 03 Apr 2021 07:40:12: 19000000 INFO @ Sat, 03 Apr 2021 07:40:14: 27000000 INFO @ Sat, 03 Apr 2021 07:40:14: 21000000 INFO @ Sat, 03 Apr 2021 07:40:21: 20000000 INFO @ Sat, 03 Apr 2021 07:40:23: 28000000 INFO @ Sat, 03 Apr 2021 07:40:24: 22000000 INFO @ Sat, 03 Apr 2021 07:40:29: 21000000 INFO @ Sat, 03 Apr 2021 07:40:31: 29000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:40:33: 23000000 INFO @ Sat, 03 Apr 2021 07:40:38: 22000000 INFO @ Sat, 03 Apr 2021 07:40:40: 30000000 INFO @ Sat, 03 Apr 2021 07:40:42: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:40:42: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:40:42: #1 total tags in treatment: 12854486 INFO @ Sat, 03 Apr 2021 07:40:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:40:42: #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 07:40:42: #1 tags after filtering in treatment: 8934073 INFO @ Sat, 03 Apr 2021 07:40:42: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:40:42: #1 finished! INFO @ Sat, 03 Apr 2021 07:40:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:40:42: 24000000 INFO @ Sat, 03 Apr 2021 07:40:43: #2 number of paired peaks: 646 WARNING @ Sat, 03 Apr 2021 07:40:43: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Sat, 03 Apr 2021 07:40:43: start model_add_line... INFO @ Sat, 03 Apr 2021 07:40:43: start X-correlation... INFO @ Sat, 03 Apr 2021 07:40:43: end of X-cor INFO @ Sat, 03 Apr 2021 07:40:43: #2 finished! INFO @ Sat, 03 Apr 2021 07:40:43: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 07:40:43: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 07:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.05_model.r WARNING @ Sat, 03 Apr 2021 07:40:43: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:40:43: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sat, 03 Apr 2021 07:40:43: #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 07:40:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:40:47: 23000000 INFO @ Sat, 03 Apr 2021 07:40:52: 25000000 INFO @ Sat, 03 Apr 2021 07:40:55: 24000000 INFO @ Sat, 03 Apr 2021 07:41:01: 26000000 INFO @ Sat, 03 Apr 2021 07:41:04: 25000000 INFO @ Sat, 03 Apr 2021 07:41:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:41:11: 27000000 INFO @ Sat, 03 Apr 2021 07:41:13: 26000000 INFO @ Sat, 03 Apr 2021 07:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.05_summits.bed INFO @ Sat, 03 Apr 2021 07:41:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6411 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:41:20: 28000000 INFO @ Sat, 03 Apr 2021 07:41:21: 27000000 INFO @ Sat, 03 Apr 2021 07:41:29: 29000000 INFO @ Sat, 03 Apr 2021 07:41:30: 28000000 INFO @ Sat, 03 Apr 2021 07:41:38: 30000000 INFO @ Sat, 03 Apr 2021 07:41:38: 29000000 INFO @ Sat, 03 Apr 2021 07:41:40: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:41:40: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:41:40: #1 total tags in treatment: 12854486 INFO @ Sat, 03 Apr 2021 07:41:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:41:40: #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 07:41:40: #1 tags after filtering in treatment: 8934073 INFO @ Sat, 03 Apr 2021 07:41:40: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:41:40: #1 finished! INFO @ Sat, 03 Apr 2021 07:41:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:41:41: #2 number of paired peaks: 646 WARNING @ Sat, 03 Apr 2021 07:41:41: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Sat, 03 Apr 2021 07:41:41: start model_add_line... INFO @ Sat, 03 Apr 2021 07:41:41: start X-correlation... INFO @ Sat, 03 Apr 2021 07:41:41: end of X-cor INFO @ Sat, 03 Apr 2021 07:41:41: #2 finished! INFO @ Sat, 03 Apr 2021 07:41:41: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 07:41:41: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 07:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.10_model.r WARNING @ Sat, 03 Apr 2021 07:41:41: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:41:41: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sat, 03 Apr 2021 07:41:41: #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 07:41:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:41:46: 30000000 INFO @ Sat, 03 Apr 2021 07:41:48: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:41:48: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:41:48: #1 total tags in treatment: 12854486 INFO @ Sat, 03 Apr 2021 07:41:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:41:48: #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 07:41:48: #1 tags after filtering in treatment: 8934073 INFO @ Sat, 03 Apr 2021 07:41:48: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:41:48: #1 finished! INFO @ Sat, 03 Apr 2021 07:41:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:41:48: #2 number of paired peaks: 646 WARNING @ Sat, 03 Apr 2021 07:41:48: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Sat, 03 Apr 2021 07:41:48: start model_add_line... INFO @ Sat, 03 Apr 2021 07:41:49: start X-correlation... INFO @ Sat, 03 Apr 2021 07:41:49: end of X-cor INFO @ Sat, 03 Apr 2021 07:41:49: #2 finished! INFO @ Sat, 03 Apr 2021 07:41:49: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 07:41:49: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Apr 2021 07:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.20_model.r WARNING @ Sat, 03 Apr 2021 07:41:49: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:41:49: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sat, 03 Apr 2021 07:41:49: #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 07:41:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:42:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:42:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.10_summits.bed INFO @ Sat, 03 Apr 2021 07:42:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3798 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:42:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:42:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:42:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029123/SRX3029123.20_summits.bed INFO @ Sat, 03 Apr 2021 07:42:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1924 records, 4 fields): 3 millis CompletedMACS2peakCalling