Job ID = 14160362 SRX = SRX9567180 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23548842 spots for SRR13125155/SRR13125155.sra Written 23548842 spots for SRR13125155/SRR13125155.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160632 ("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: 01:08:28 23548842 reads; of these: 23548842 (100.00%) were paired; of these: 8247553 (35.02%) aligned concordantly 0 times 8584171 (36.45%) aligned concordantly exactly 1 time 6717118 (28.52%) aligned concordantly >1 times ---- 8247553 pairs aligned concordantly 0 times; of these: 4063303 (49.27%) aligned discordantly 1 time ---- 4184250 pairs aligned 0 times concordantly or discordantly; of these: 8368500 mates make up the pairs; of these: 6172761 (73.76%) aligned 0 times 903729 (10.80%) aligned exactly 1 time 1292010 (15.44%) aligned >1 times 86.89% overall alignment rate Time searching: 01:08:28 Overall time: 01:08:28 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] 15209857 / 19338542 = 0.7865 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 03:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.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 03:07:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:22: 1000000 INFO @ Thu, 09 Dec 2021 03:07:32: 2000000 INFO @ Thu, 09 Dec 2021 03:07:41: 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 03:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.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 03:07:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:51: 4000000 INFO @ Thu, 09 Dec 2021 03:07:52: 1000000 INFO @ Thu, 09 Dec 2021 03:08:01: 2000000 INFO @ Thu, 09 Dec 2021 03:08:01: 5000000 INFO @ Thu, 09 Dec 2021 03:08:09: 3000000 INFO @ Thu, 09 Dec 2021 03:08:10: 6000000 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 03:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.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 03:08:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:08:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:18: 4000000 INFO @ Thu, 09 Dec 2021 03:08:20: 7000000 INFO @ Thu, 09 Dec 2021 03:08:22: 1000000 INFO @ Thu, 09 Dec 2021 03:08:27: 5000000 INFO @ Thu, 09 Dec 2021 03:08:30: 8000000 INFO @ Thu, 09 Dec 2021 03:08:31: 2000000 INFO @ Thu, 09 Dec 2021 03:08:36: 6000000 INFO @ Thu, 09 Dec 2021 03:08:40: 9000000 INFO @ Thu, 09 Dec 2021 03:08:40: 3000000 INFO @ Thu, 09 Dec 2021 03:08:45: 7000000 INFO @ Thu, 09 Dec 2021 03:08:49: 4000000 INFO @ Thu, 09 Dec 2021 03:08:49: 10000000 INFO @ Thu, 09 Dec 2021 03:08:54: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:08:54: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:08:54: #1 total tags in treatment: 3275119 INFO @ Thu, 09 Dec 2021 03:08:54: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:08:54: #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 03:08:54: #1 tags after filtering in treatment: 2132387 INFO @ Thu, 09 Dec 2021 03:08:54: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 09 Dec 2021 03:08:54: #1 finished! INFO @ Thu, 09 Dec 2021 03:08:54: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:08:54: 8000000 INFO @ Thu, 09 Dec 2021 03:08:54: #2 number of paired peaks: 918 WARNING @ Thu, 09 Dec 2021 03:08:54: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Thu, 09 Dec 2021 03:08:54: start model_add_line... INFO @ Thu, 09 Dec 2021 03:08:54: start X-correlation... INFO @ Thu, 09 Dec 2021 03:08:54: end of X-cor INFO @ Thu, 09 Dec 2021 03:08:54: #2 finished! INFO @ Thu, 09 Dec 2021 03:08:54: #2 predicted fragment length is 294 bps INFO @ Thu, 09 Dec 2021 03:08:54: #2 alternative fragment length(s) may be 294 bps INFO @ Thu, 09 Dec 2021 03:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.05_model.r WARNING @ Thu, 09 Dec 2021 03:08:54: #2 Since the d (294) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:08:54: #2 You may need to consider one of the other alternative d(s): 294 WARNING @ Thu, 09 Dec 2021 03:08:54: #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 03:08:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:08:57: 5000000 INFO @ Thu, 09 Dec 2021 03:09:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:03: 9000000 INFO @ Thu, 09 Dec 2021 03:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.05_summits.bed INFO @ Thu, 09 Dec 2021 03:09:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (680 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:09:06: 6000000 INFO @ Thu, 09 Dec 2021 03:09:11: 10000000 INFO @ Thu, 09 Dec 2021 03:09:14: 7000000 INFO @ Thu, 09 Dec 2021 03:09:15: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:15: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:15: #1 total tags in treatment: 3275119 INFO @ Thu, 09 Dec 2021 03:09:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:15: #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 03:09:15: #1 tags after filtering in treatment: 2132387 INFO @ Thu, 09 Dec 2021 03:09:15: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 09 Dec 2021 03:09:15: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:16: #2 number of paired peaks: 918 WARNING @ Thu, 09 Dec 2021 03:09:16: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:16: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:16: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:16: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:16: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:16: #2 predicted fragment length is 294 bps INFO @ Thu, 09 Dec 2021 03:09:16: #2 alternative fragment length(s) may be 294 bps INFO @ Thu, 09 Dec 2021 03:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.10_model.r WARNING @ Thu, 09 Dec 2021 03:09:16: #2 Since the d (294) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:16: #2 You may need to consider one of the other alternative d(s): 294 WARNING @ Thu, 09 Dec 2021 03:09:16: #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 03:09:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:09:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:22: 8000000 INFO @ Thu, 09 Dec 2021 03:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.10_summits.bed INFO @ Thu, 09 Dec 2021 03:09:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:09:30: 9000000 INFO @ Thu, 09 Dec 2021 03:09:37: 10000000 INFO @ Thu, 09 Dec 2021 03:09:41: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:41: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:41: #1 total tags in treatment: 3275119 INFO @ Thu, 09 Dec 2021 03:09:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:41: #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 03:09:41: #1 tags after filtering in treatment: 2132387 INFO @ Thu, 09 Dec 2021 03:09:41: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 09 Dec 2021 03:09:41: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:41: #2 number of paired peaks: 918 WARNING @ Thu, 09 Dec 2021 03:09:41: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:41: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:41: #2 predicted fragment length is 294 bps INFO @ Thu, 09 Dec 2021 03:09:41: #2 alternative fragment length(s) may be 294 bps INFO @ Thu, 09 Dec 2021 03:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.20_model.r WARNING @ Thu, 09 Dec 2021 03:09:41: #2 Since the d (294) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:41: #2 You may need to consider one of the other alternative d(s): 294 WARNING @ Thu, 09 Dec 2021 03:09:41: #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 03:09:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:09:47: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567180/SRX9567180.20_summits.bed INFO @ Thu, 09 Dec 2021 03:09:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 2 millis CompletedMACS2peakCalling