Job ID = 14160355 SRX = SRX9567179 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18267621 spots for SRR13125154/SRR13125154.sra Written 18267621 spots for SRR13125154/SRR13125154.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160564 ("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: 00:43:56 18267621 reads; of these: 18267621 (100.00%) were paired; of these: 8416972 (46.08%) aligned concordantly 0 times 7652605 (41.89%) aligned concordantly exactly 1 time 2198044 (12.03%) aligned concordantly >1 times ---- 8416972 pairs aligned concordantly 0 times; of these: 4650268 (55.25%) aligned discordantly 1 time ---- 3766704 pairs aligned 0 times concordantly or discordantly; of these: 7533408 mates make up the pairs; of these: 5347934 (70.99%) aligned 0 times 1034366 (13.73%) aligned exactly 1 time 1151108 (15.28%) aligned >1 times 85.36% overall alignment rate Time searching: 00:43:56 Overall time: 00:43:56 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] 12120427 / 14490937 = 0.8364 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 02:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.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 02:37:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:37:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:37:23: 1000000 INFO @ Thu, 09 Dec 2021 02:37:34: 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 02:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.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 02:37:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:37:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:37:45: 3000000 INFO @ Thu, 09 Dec 2021 02:37:53: 1000000 INFO @ Thu, 09 Dec 2021 02:37:57: 4000000 INFO @ Thu, 09 Dec 2021 02:38:04: 2000000 INFO @ Thu, 09 Dec 2021 02:38:10: 5000000 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 02:38:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.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 02:38:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:38:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:38:15: 3000000 INFO @ Thu, 09 Dec 2021 02:38:22: 6000000 INFO @ Thu, 09 Dec 2021 02:38:26: 1000000 INFO @ Thu, 09 Dec 2021 02:38:27: 4000000 INFO @ Thu, 09 Dec 2021 02:38:35: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:38:35: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:38:35: #1 total tags in treatment: 1676079 INFO @ Thu, 09 Dec 2021 02:38:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:38:35: #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 02:38:35: #1 tags after filtering in treatment: 1368830 INFO @ Thu, 09 Dec 2021 02:38:35: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 09 Dec 2021 02:38:35: #1 finished! INFO @ Thu, 09 Dec 2021 02:38:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:38:35: #2 number of paired peaks: 922 WARNING @ Thu, 09 Dec 2021 02:38:35: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Thu, 09 Dec 2021 02:38:35: start model_add_line... INFO @ Thu, 09 Dec 2021 02:38:35: start X-correlation... INFO @ Thu, 09 Dec 2021 02:38:35: end of X-cor INFO @ Thu, 09 Dec 2021 02:38:35: #2 finished! INFO @ Thu, 09 Dec 2021 02:38:35: #2 predicted fragment length is 270 bps INFO @ Thu, 09 Dec 2021 02:38:35: #2 alternative fragment length(s) may be 270 bps INFO @ Thu, 09 Dec 2021 02:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.05_model.r WARNING @ Thu, 09 Dec 2021 02:38:35: #2 Since the d (270) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:38:35: #2 You may need to consider one of the other alternative d(s): 270 WARNING @ Thu, 09 Dec 2021 02:38:35: #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 02:38:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:38:39: 5000000 INFO @ Thu, 09 Dec 2021 02:38:39: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:38:40: 2000000 INFO @ Thu, 09 Dec 2021 02:38:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:38:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:38:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.05_summits.bed INFO @ Thu, 09 Dec 2021 02:38:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:38:50: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:38:53: 3000000 INFO @ Thu, 09 Dec 2021 02:39:01: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:39:01: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:39:01: #1 total tags in treatment: 1676079 INFO @ Thu, 09 Dec 2021 02:39:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:39:01: #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 02:39:01: #1 tags after filtering in treatment: 1368830 INFO @ Thu, 09 Dec 2021 02:39:01: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 09 Dec 2021 02:39:01: #1 finished! INFO @ Thu, 09 Dec 2021 02:39:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:39:01: #2 number of paired peaks: 922 WARNING @ Thu, 09 Dec 2021 02:39:01: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Thu, 09 Dec 2021 02:39:01: start model_add_line... INFO @ Thu, 09 Dec 2021 02:39:01: start X-correlation... INFO @ Thu, 09 Dec 2021 02:39:01: end of X-cor INFO @ Thu, 09 Dec 2021 02:39:01: #2 finished! INFO @ Thu, 09 Dec 2021 02:39:01: #2 predicted fragment length is 270 bps INFO @ Thu, 09 Dec 2021 02:39:01: #2 alternative fragment length(s) may be 270 bps INFO @ Thu, 09 Dec 2021 02:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.10_model.r WARNING @ Thu, 09 Dec 2021 02:39:01: #2 Since the d (270) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:39:01: #2 You may need to consider one of the other alternative d(s): 270 WARNING @ Thu, 09 Dec 2021 02:39:01: #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 02:39:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:39:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:39:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:39:06: 4000000 INFO @ Thu, 09 Dec 2021 02:39:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:39:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:39:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.10_summits.bed INFO @ Thu, 09 Dec 2021 02:39:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:39:17: 5000000 INFO @ Thu, 09 Dec 2021 02:39:28: 6000000 INFO @ Thu, 09 Dec 2021 02:39:39: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:39:39: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:39:39: #1 total tags in treatment: 1676079 INFO @ Thu, 09 Dec 2021 02:39:39: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:39:39: #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 02:39:39: #1 tags after filtering in treatment: 1368830 INFO @ Thu, 09 Dec 2021 02:39:39: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 09 Dec 2021 02:39:39: #1 finished! INFO @ Thu, 09 Dec 2021 02:39:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:39:39: #2 number of paired peaks: 922 WARNING @ Thu, 09 Dec 2021 02:39:39: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Thu, 09 Dec 2021 02:39:39: start model_add_line... INFO @ Thu, 09 Dec 2021 02:39:39: start X-correlation... INFO @ Thu, 09 Dec 2021 02:39:39: end of X-cor INFO @ Thu, 09 Dec 2021 02:39:39: #2 finished! INFO @ Thu, 09 Dec 2021 02:39:39: #2 predicted fragment length is 270 bps INFO @ Thu, 09 Dec 2021 02:39:39: #2 alternative fragment length(s) may be 270 bps INFO @ Thu, 09 Dec 2021 02:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.20_model.r WARNING @ Thu, 09 Dec 2021 02:39:39: #2 Since the d (270) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:39:39: #2 You may need to consider one of the other alternative d(s): 270 WARNING @ Thu, 09 Dec 2021 02:39:39: #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 02:39:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:39:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567179/SRX9567179.20_summits.bed INFO @ Thu, 09 Dec 2021 02:39:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (314 records, 4 fields): 2 millis CompletedMACS2peakCalling