Job ID = 14160372 SRX = SRX9567188 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26401687 spots for SRR13125163/SRR13125163.sra Written 26401687 spots for SRR13125163/SRR13125163.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160639 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:59:36 26401687 reads; of these: 26401687 (100.00%) were paired; of these: 10850068 (41.10%) aligned concordantly 0 times 13463575 (51.00%) aligned concordantly exactly 1 time 2088044 (7.91%) aligned concordantly >1 times ---- 10850068 pairs aligned concordantly 0 times; of these: 4745477 (43.74%) aligned discordantly 1 time ---- 6104591 pairs aligned 0 times concordantly or discordantly; of these: 12209182 mates make up the pairs; of these: 9877310 (80.90%) aligned 0 times 1199126 (9.82%) aligned exactly 1 time 1132746 (9.28%) aligned >1 times 81.29% overall alignment rate Time searching: 00:59:37 Overall time: 00:59:37 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 32 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] 16491582 / 20273242 = 0.8135 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 03:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.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 03:14:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:14:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:14:40: 1000000 INFO @ Thu, 09 Dec 2021 03:14:51: 2000000 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 03:14:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.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 03:14:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:14:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:15:03: 3000000 INFO @ Thu, 09 Dec 2021 03:15:16: 4000000 INFO @ Thu, 09 Dec 2021 03:15:17: 1000000 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 03:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.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 03:15:27: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:15:27: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:15:29: 5000000 INFO @ Thu, 09 Dec 2021 03:15:36: 2000000 INFO @ Thu, 09 Dec 2021 03:15:42: 6000000 INFO @ Thu, 09 Dec 2021 03:15:42: 1000000 INFO @ Thu, 09 Dec 2021 03:15:55: 7000000 INFO @ Thu, 09 Dec 2021 03:15:57: 3000000 INFO @ Thu, 09 Dec 2021 03:15:58: 2000000 INFO @ Thu, 09 Dec 2021 03:16:08: 8000000 INFO @ Thu, 09 Dec 2021 03:16:13: 3000000 INFO @ Thu, 09 Dec 2021 03:16:16: 4000000 INFO @ Thu, 09 Dec 2021 03:16:21: 9000000 INFO @ Thu, 09 Dec 2021 03:16:28: 4000000 INFO @ Thu, 09 Dec 2021 03:16:32: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:16:32: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:16:32: #1 total tags in treatment: 2923299 INFO @ Thu, 09 Dec 2021 03:16:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:16:32: #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 03:16:33: #1 tags after filtering in treatment: 2615060 INFO @ Thu, 09 Dec 2021 03:16:33: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 03:16:33: #1 finished! INFO @ Thu, 09 Dec 2021 03:16:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:16:33: #2 number of paired peaks: 666 WARNING @ Thu, 09 Dec 2021 03:16:33: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Thu, 09 Dec 2021 03:16:33: start model_add_line... INFO @ Thu, 09 Dec 2021 03:16:33: start X-correlation... INFO @ Thu, 09 Dec 2021 03:16:33: end of X-cor INFO @ Thu, 09 Dec 2021 03:16:33: #2 finished! INFO @ Thu, 09 Dec 2021 03:16:33: #2 predicted fragment length is 231 bps INFO @ Thu, 09 Dec 2021 03:16:33: #2 alternative fragment length(s) may be 231 bps INFO @ Thu, 09 Dec 2021 03:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.05_model.r WARNING @ Thu, 09 Dec 2021 03:16:33: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:16:33: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Thu, 09 Dec 2021 03:16:33: #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 03:16:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:16:35: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:16:43: 5000000 INFO @ Thu, 09 Dec 2021 03:16:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.05_summits.bed INFO @ Thu, 09 Dec 2021 03:16:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:16:54: 6000000 INFO @ Thu, 09 Dec 2021 03:16:57: 6000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:17:12: 7000000 INFO @ Thu, 09 Dec 2021 03:17:13: 7000000 INFO @ Thu, 09 Dec 2021 03:17:26: 8000000 INFO @ Thu, 09 Dec 2021 03:17:32: 8000000 INFO @ Thu, 09 Dec 2021 03:17:41: 9000000 INFO @ Thu, 09 Dec 2021 03:17:51: 9000000 INFO @ Thu, 09 Dec 2021 03:17:54: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:17:54: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:17:54: #1 total tags in treatment: 2923299 INFO @ Thu, 09 Dec 2021 03:17:54: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:54: #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 03:17:54: #1 tags after filtering in treatment: 2615060 INFO @ Thu, 09 Dec 2021 03:17:54: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 03:17:54: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:54: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:54: #2 number of paired peaks: 666 WARNING @ Thu, 09 Dec 2021 03:17:54: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Thu, 09 Dec 2021 03:17:54: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:54: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:54: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:54: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:54: #2 predicted fragment length is 231 bps INFO @ Thu, 09 Dec 2021 03:17:54: #2 alternative fragment length(s) may be 231 bps INFO @ Thu, 09 Dec 2021 03:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.20_model.r WARNING @ Thu, 09 Dec 2021 03:17:54: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:17:54: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Thu, 09 Dec 2021 03:17:54: #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 03:17:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:18:04: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:07: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:18:07: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:18:07: #1 total tags in treatment: 2923299 INFO @ Thu, 09 Dec 2021 03:18:07: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:18:07: #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 03:18:07: #1 tags after filtering in treatment: 2615060 INFO @ Thu, 09 Dec 2021 03:18:07: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 03:18:07: #1 finished! INFO @ Thu, 09 Dec 2021 03:18:07: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:18:07: #2 number of paired peaks: 666 WARNING @ Thu, 09 Dec 2021 03:18:07: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Thu, 09 Dec 2021 03:18:07: start model_add_line... INFO @ Thu, 09 Dec 2021 03:18:07: start X-correlation... INFO @ Thu, 09 Dec 2021 03:18:07: end of X-cor INFO @ Thu, 09 Dec 2021 03:18:07: #2 finished! INFO @ Thu, 09 Dec 2021 03:18:07: #2 predicted fragment length is 231 bps INFO @ Thu, 09 Dec 2021 03:18:07: #2 alternative fragment length(s) may be 231 bps INFO @ Thu, 09 Dec 2021 03:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.10_model.r WARNING @ Thu, 09 Dec 2021 03:18:07: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:18:07: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Thu, 09 Dec 2021 03:18:07: #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 03:18:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:18:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.20_summits.bed INFO @ Thu, 09 Dec 2021 03:18:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:18:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567188/SRX9567188.10_summits.bed INFO @ Thu, 09 Dec 2021 03:18:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 2 millis CompletedMACS2peakCalling