Job ID = 14160564 SRX = SRX9567179 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: 00:38:15 18267621 reads; of these: 18267621 (100.00%) were paired; of these: 8416953 (46.08%) aligned concordantly 0 times 7652605 (41.89%) aligned concordantly exactly 1 time 2198063 (12.03%) aligned concordantly >1 times ---- 8416953 pairs aligned concordantly 0 times; of these: 4650358 (55.25%) aligned discordantly 1 time ---- 3766595 pairs aligned 0 times concordantly or discordantly; of these: 7533190 mates make up the pairs; of these: 5347788 (70.99%) aligned 0 times 1034313 (13.73%) aligned exactly 1 time 1151089 (15.28%) aligned >1 times 85.36% overall alignment rate Time searching: 00:38:15 Overall time: 00:38:15 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] 12120633 / 14491044 = 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 03:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 03:58:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:58:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:58:53: 1000000 INFO @ Thu, 09 Dec 2021 03:59:00: 2000000 INFO @ Thu, 09 Dec 2021 03:59:08: 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 03:59:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 03:59:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:16: 4000000 INFO @ Thu, 09 Dec 2021 03:59:26: 5000000 INFO @ Thu, 09 Dec 2021 03:59:26: 1000000 INFO @ Thu, 09 Dec 2021 03:59:36: 6000000 INFO @ Thu, 09 Dec 2021 03:59:37: 2000000 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 03:59:45: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:59:45: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:59:45: #1 total tags in treatment: 1675978 INFO @ Thu, 09 Dec 2021 03:59:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:59:45: #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 03:59:45: #1 tags after filtering in treatment: 1368851 INFO @ Thu, 09 Dec 2021 03:59:45: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 09 Dec 2021 03:59:45: #1 finished! INFO @ Thu, 09 Dec 2021 03:59:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:59:45: #2 number of paired peaks: 922 WARNING @ Thu, 09 Dec 2021 03:59:45: 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 03:59:45: start model_add_line... INFO @ Thu, 09 Dec 2021 03:59:45: start X-correlation... INFO @ Thu, 09 Dec 2021 03:59:45: end of X-cor INFO @ Thu, 09 Dec 2021 03:59:45: #2 finished! INFO @ Thu, 09 Dec 2021 03:59:45: #2 predicted fragment length is 270 bps INFO @ Thu, 09 Dec 2021 03:59:45: #2 alternative fragment length(s) may be 270 bps INFO @ Thu, 09 Dec 2021 03:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.05_model.r WARNING @ Thu, 09 Dec 2021 03:59:45: #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 03:59:45: #2 You may need to consider one of the other alternative d(s): 270 WARNING @ Thu, 09 Dec 2021 03:59:45: #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 03:59:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 03:59:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:48: 3000000 INFO @ Thu, 09 Dec 2021 03:59:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.05_summits.bed INFO @ Thu, 09 Dec 2021 03:59:51: 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 03:59:57: 1000000 INFO @ Thu, 09 Dec 2021 03:59:59: 4000000 INFO @ Thu, 09 Dec 2021 04:00:08: 2000000 INFO @ Thu, 09 Dec 2021 04:00:10: 5000000 INFO @ Thu, 09 Dec 2021 04:00:19: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:00:21: 6000000 INFO @ Thu, 09 Dec 2021 04:00:31: 4000000 INFO @ Thu, 09 Dec 2021 04:00:32: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:00:32: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:00:32: #1 total tags in treatment: 1675978 INFO @ Thu, 09 Dec 2021 04:00:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:00:32: #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 04:00:32: #1 tags after filtering in treatment: 1368851 INFO @ Thu, 09 Dec 2021 04:00:32: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 09 Dec 2021 04:00:32: #1 finished! INFO @ Thu, 09 Dec 2021 04:00:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:00:32: #2 number of paired peaks: 922 WARNING @ Thu, 09 Dec 2021 04:00:32: 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 04:00:32: start model_add_line... INFO @ Thu, 09 Dec 2021 04:00:32: start X-correlation... INFO @ Thu, 09 Dec 2021 04:00:32: end of X-cor INFO @ Thu, 09 Dec 2021 04:00:32: #2 finished! INFO @ Thu, 09 Dec 2021 04:00:32: #2 predicted fragment length is 270 bps INFO @ Thu, 09 Dec 2021 04:00:32: #2 alternative fragment length(s) may be 270 bps INFO @ Thu, 09 Dec 2021 04:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.10_model.r WARNING @ Thu, 09 Dec 2021 04:00:32: #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 04:00:32: #2 You may need to consider one of the other alternative d(s): 270 WARNING @ Thu, 09 Dec 2021 04:00:32: #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 04:00:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:00:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:00:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.10_summits.bed INFO @ Thu, 09 Dec 2021 04:00:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:00:41: 5000000 INFO @ Thu, 09 Dec 2021 04:00:50: 6000000 INFO @ Thu, 09 Dec 2021 04:00:59: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:00:59: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:00:59: #1 total tags in treatment: 1675978 INFO @ Thu, 09 Dec 2021 04:00:59: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:00:59: #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 04:00:59: #1 tags after filtering in treatment: 1368851 INFO @ Thu, 09 Dec 2021 04:00:59: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 09 Dec 2021 04:00:59: #1 finished! INFO @ Thu, 09 Dec 2021 04:00:59: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:01:00: #2 number of paired peaks: 922 WARNING @ Thu, 09 Dec 2021 04:01:00: 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 04:01:00: start model_add_line... INFO @ Thu, 09 Dec 2021 04:01:00: start X-correlation... INFO @ Thu, 09 Dec 2021 04:01:00: end of X-cor INFO @ Thu, 09 Dec 2021 04:01:00: #2 finished! INFO @ Thu, 09 Dec 2021 04:01:00: #2 predicted fragment length is 270 bps INFO @ Thu, 09 Dec 2021 04:01:00: #2 alternative fragment length(s) may be 270 bps INFO @ Thu, 09 Dec 2021 04:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.20_model.r WARNING @ Thu, 09 Dec 2021 04:01:00: #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 04:01:00: #2 You may need to consider one of the other alternative d(s): 270 WARNING @ Thu, 09 Dec 2021 04:01:00: #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 04:01:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:01:04: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567179/SRX9567179.20_summits.bed INFO @ Thu, 09 Dec 2021 04:01:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 1 millis CompletedMACS2peakCalling