Job ID = 14160626 SRX = SRX9567187 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: 01:06:32 28561580 reads; of these: 28561580 (100.00%) were paired; of these: 8512994 (29.81%) aligned concordantly 0 times 17340181 (60.71%) aligned concordantly exactly 1 time 2708405 (9.48%) aligned concordantly >1 times ---- 8512994 pairs aligned concordantly 0 times; of these: 6113557 (71.81%) aligned discordantly 1 time ---- 2399437 pairs aligned 0 times concordantly or discordantly; of these: 4798874 mates make up the pairs; of these: 1998471 (41.64%) aligned 0 times 1375010 (28.65%) aligned exactly 1 time 1425393 (29.70%) aligned >1 times 96.50% overall alignment rate Time searching: 01:06:32 Overall time: 01:06:32 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 40 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] 17969543 / 26137323 = 0.6875 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 @ Thu, 09 Dec 2021 04:48:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.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 @ Thu, 09 Dec 2021 04:48:52: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:48:52: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:49:01: 1000000 INFO @ Thu, 09 Dec 2021 04:49:09: 2000000 INFO @ Thu, 09 Dec 2021 04:49:18: 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 @ Thu, 09 Dec 2021 04:49:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.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 @ Thu, 09 Dec 2021 04:49:22: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:49:22: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:49:27: 4000000 INFO @ Thu, 09 Dec 2021 04:49:31: 1000000 INFO @ Thu, 09 Dec 2021 04:49:36: 5000000 INFO @ Thu, 09 Dec 2021 04:49:40: 2000000 INFO @ Thu, 09 Dec 2021 04:49:45: 6000000 INFO @ Thu, 09 Dec 2021 04:49:49: 3000000 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 @ Thu, 09 Dec 2021 04:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.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 @ Thu, 09 Dec 2021 04:49:52: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:49:52: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:49:54: 7000000 INFO @ Thu, 09 Dec 2021 04:49:58: 4000000 INFO @ Thu, 09 Dec 2021 04:50:01: 1000000 INFO @ Thu, 09 Dec 2021 04:50:03: 8000000 INFO @ Thu, 09 Dec 2021 04:50:06: 5000000 INFO @ Thu, 09 Dec 2021 04:50:11: 2000000 INFO @ Thu, 09 Dec 2021 04:50:13: 9000000 INFO @ Thu, 09 Dec 2021 04:50:15: 6000000 INFO @ Thu, 09 Dec 2021 04:50:20: 3000000 INFO @ Thu, 09 Dec 2021 04:50:22: 10000000 INFO @ Thu, 09 Dec 2021 04:50:24: 7000000 INFO @ Thu, 09 Dec 2021 04:50:30: 4000000 INFO @ Thu, 09 Dec 2021 04:50:31: 11000000 INFO @ Thu, 09 Dec 2021 04:50:33: 8000000 INFO @ Thu, 09 Dec 2021 04:50:39: 5000000 INFO @ Thu, 09 Dec 2021 04:50:40: 12000000 INFO @ Thu, 09 Dec 2021 04:50:42: 9000000 INFO @ Thu, 09 Dec 2021 04:50:49: 6000000 INFO @ Thu, 09 Dec 2021 04:50:49: 13000000 INFO @ Thu, 09 Dec 2021 04:50:51: 10000000 INFO @ Thu, 09 Dec 2021 04:50:58: 14000000 INFO @ Thu, 09 Dec 2021 04:50:58: 7000000 INFO @ Thu, 09 Dec 2021 04:51:01: 11000000 INFO @ Thu, 09 Dec 2021 04:51:07: 15000000 INFO @ Thu, 09 Dec 2021 04:51:07: 8000000 INFO @ Thu, 09 Dec 2021 04:51:10: 12000000 INFO @ Thu, 09 Dec 2021 04:51:16: 16000000 INFO @ Thu, 09 Dec 2021 04:51:17: 9000000 INFO @ Thu, 09 Dec 2021 04:51:19: 13000000 INFO @ Thu, 09 Dec 2021 04:51:25: 17000000 INFO @ Thu, 09 Dec 2021 04:51:26: 10000000 INFO @ Thu, 09 Dec 2021 04:51:27: 14000000 INFO @ Thu, 09 Dec 2021 04:51:34: 18000000 INFO @ Thu, 09 Dec 2021 04:51:36: 11000000 INFO @ Thu, 09 Dec 2021 04:51:36: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:51:43: 19000000 INFO @ Thu, 09 Dec 2021 04:51:45: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:51:45: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:51:45: #1 total tags in treatment: 6376452 INFO @ Thu, 09 Dec 2021 04:51:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:51:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:51:45: #1 tags after filtering in treatment: 5790851 INFO @ Thu, 09 Dec 2021 04:51:45: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 04:51:45: #1 finished! INFO @ Thu, 09 Dec 2021 04:51:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:51:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:51:45: 16000000 INFO @ Thu, 09 Dec 2021 04:51:45: 12000000 INFO @ Thu, 09 Dec 2021 04:51:46: #2 number of paired peaks: 599 WARNING @ Thu, 09 Dec 2021 04:51:46: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Thu, 09 Dec 2021 04:51:46: start model_add_line... INFO @ Thu, 09 Dec 2021 04:51:46: start X-correlation... INFO @ Thu, 09 Dec 2021 04:51:46: end of X-cor INFO @ Thu, 09 Dec 2021 04:51:46: #2 finished! INFO @ Thu, 09 Dec 2021 04:51:46: #2 predicted fragment length is 226 bps INFO @ Thu, 09 Dec 2021 04:51:46: #2 alternative fragment length(s) may be 226 bps INFO @ Thu, 09 Dec 2021 04:51:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.05_model.r WARNING @ Thu, 09 Dec 2021 04:51:46: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:51:46: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Thu, 09 Dec 2021 04:51:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:51:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:51:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:51:54: 17000000 INFO @ Thu, 09 Dec 2021 04:51:54: 13000000 INFO @ Thu, 09 Dec 2021 04:52:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:52:03: 18000000 INFO @ Thu, 09 Dec 2021 04:52:03: 14000000 INFO @ Thu, 09 Dec 2021 04:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.05_summits.bed INFO @ Thu, 09 Dec 2021 04:52:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:52:12: 19000000 INFO @ Thu, 09 Dec 2021 04:52:12: 15000000 INFO @ Thu, 09 Dec 2021 04:52:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:52:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:52:13: #1 total tags in treatment: 6376452 INFO @ Thu, 09 Dec 2021 04:52:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:52:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:52:14: #1 tags after filtering in treatment: 5790851 INFO @ Thu, 09 Dec 2021 04:52:14: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 04:52:14: #1 finished! INFO @ Thu, 09 Dec 2021 04:52:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:52:14: #2 number of paired peaks: 599 WARNING @ Thu, 09 Dec 2021 04:52:14: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Thu, 09 Dec 2021 04:52:14: start model_add_line... INFO @ Thu, 09 Dec 2021 04:52:14: start X-correlation... INFO @ Thu, 09 Dec 2021 04:52:14: end of X-cor INFO @ Thu, 09 Dec 2021 04:52:14: #2 finished! INFO @ Thu, 09 Dec 2021 04:52:14: #2 predicted fragment length is 226 bps INFO @ Thu, 09 Dec 2021 04:52:14: #2 alternative fragment length(s) may be 226 bps INFO @ Thu, 09 Dec 2021 04:52:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.10_model.r WARNING @ Thu, 09 Dec 2021 04:52:14: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:52:14: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Thu, 09 Dec 2021 04:52:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:52:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:52:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:52:20: 16000000 INFO @ Thu, 09 Dec 2021 04:52:29: 17000000 INFO @ Thu, 09 Dec 2021 04:52:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.10_summits.bed INFO @ Thu, 09 Dec 2021 04:52:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:52:37: 18000000 INFO @ Thu, 09 Dec 2021 04:52:45: 19000000 INFO @ Thu, 09 Dec 2021 04:52:47: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:52:47: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:52:47: #1 total tags in treatment: 6376452 INFO @ Thu, 09 Dec 2021 04:52:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:52:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:52:47: #1 tags after filtering in treatment: 5790851 INFO @ Thu, 09 Dec 2021 04:52:47: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 04:52:47: #1 finished! INFO @ Thu, 09 Dec 2021 04:52:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:52:47: #2 number of paired peaks: 599 WARNING @ Thu, 09 Dec 2021 04:52:47: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Thu, 09 Dec 2021 04:52:47: start model_add_line... INFO @ Thu, 09 Dec 2021 04:52:47: start X-correlation... INFO @ Thu, 09 Dec 2021 04:52:47: end of X-cor INFO @ Thu, 09 Dec 2021 04:52:47: #2 finished! INFO @ Thu, 09 Dec 2021 04:52:47: #2 predicted fragment length is 226 bps INFO @ Thu, 09 Dec 2021 04:52:47: #2 alternative fragment length(s) may be 226 bps INFO @ Thu, 09 Dec 2021 04:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.20_model.r WARNING @ Thu, 09 Dec 2021 04:52:47: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:52:47: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Thu, 09 Dec 2021 04:52:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:52:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:53:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567187/SRX9567187.20_summits.bed INFO @ Thu, 09 Dec 2021 04:53:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling