Job ID = 14160370 SRX = SRX9567186 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26681991 spots for SRR13125161/SRR13125161.sra Written 26681991 spots for SRR13125161/SRR13125161.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160608 ("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: 00:53:51 26681991 reads; of these: 26681991 (100.00%) were paired; of these: 7754362 (29.06%) aligned concordantly 0 times 16358800 (61.31%) aligned concordantly exactly 1 time 2568829 (9.63%) aligned concordantly >1 times ---- 7754362 pairs aligned concordantly 0 times; of these: 5238471 (67.56%) aligned discordantly 1 time ---- 2515891 pairs aligned 0 times concordantly or discordantly; of these: 5031782 mates make up the pairs; of these: 2475339 (49.19%) aligned 0 times 1308338 (26.00%) aligned exactly 1 time 1248105 (24.80%) aligned >1 times 95.36% overall alignment rate Time searching: 00:53:51 Overall time: 00:53:51 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] 19432120 / 24133870 = 0.8052 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 03:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.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 03:00:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:00:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:00:13: 1000000 INFO @ Thu, 09 Dec 2021 03:00:24: 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 03:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.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 03:00:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:00:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:00:34: 3000000 INFO @ Thu, 09 Dec 2021 03:00:44: 1000000 INFO @ Thu, 09 Dec 2021 03:00:46: 4000000 INFO @ Thu, 09 Dec 2021 03:00:55: 2000000 INFO @ Thu, 09 Dec 2021 03:00:58: 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 03:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.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 03:01:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:01:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:01:06: 3000000 INFO @ Thu, 09 Dec 2021 03:01:10: 6000000 INFO @ Thu, 09 Dec 2021 03:01:15: 1000000 INFO @ Thu, 09 Dec 2021 03:01:18: 4000000 INFO @ Thu, 09 Dec 2021 03:01:22: 7000000 INFO @ Thu, 09 Dec 2021 03:01:27: 2000000 INFO @ Thu, 09 Dec 2021 03:01:29: 5000000 INFO @ Thu, 09 Dec 2021 03:01:35: 8000000 INFO @ Thu, 09 Dec 2021 03:01:39: 3000000 INFO @ Thu, 09 Dec 2021 03:01:41: 6000000 INFO @ Thu, 09 Dec 2021 03:01:47: 9000000 INFO @ Thu, 09 Dec 2021 03:01:52: 4000000 INFO @ Thu, 09 Dec 2021 03:01:52: 7000000 INFO @ Thu, 09 Dec 2021 03:02:00: 10000000 INFO @ Thu, 09 Dec 2021 03:02:04: 8000000 INFO @ Thu, 09 Dec 2021 03:02:04: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:02:12: 11000000 INFO @ Thu, 09 Dec 2021 03:02:15: 9000000 INFO @ Thu, 09 Dec 2021 03:02:17: 6000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:02:24: 12000000 INFO @ Thu, 09 Dec 2021 03:02:24: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:02:24: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:02:24: #1 total tags in treatment: 3700191 INFO @ Thu, 09 Dec 2021 03:02:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:02:24: #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 03:02:24: #1 tags after filtering in treatment: 3341172 INFO @ Thu, 09 Dec 2021 03:02:24: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:02:24: #1 finished! INFO @ Thu, 09 Dec 2021 03:02:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:02:25: #2 number of paired peaks: 734 WARNING @ Thu, 09 Dec 2021 03:02:25: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Thu, 09 Dec 2021 03:02:25: start model_add_line... INFO @ Thu, 09 Dec 2021 03:02:25: start X-correlation... INFO @ Thu, 09 Dec 2021 03:02:25: end of X-cor INFO @ Thu, 09 Dec 2021 03:02:25: #2 finished! INFO @ Thu, 09 Dec 2021 03:02:25: #2 predicted fragment length is 227 bps INFO @ Thu, 09 Dec 2021 03:02:25: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 09 Dec 2021 03:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.05_model.r WARNING @ Thu, 09 Dec 2021 03:02:25: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:02:25: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Thu, 09 Dec 2021 03:02:25: #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 03:02:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:02:26: 10000000 INFO @ Thu, 09 Dec 2021 03:02:29: 7000000 INFO @ Thu, 09 Dec 2021 03:02:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.05_summits.bed INFO @ Thu, 09 Dec 2021 03:02:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (491 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:02:37: 11000000 INFO @ Thu, 09 Dec 2021 03:02:41: 8000000 INFO @ Thu, 09 Dec 2021 03:02:48: 12000000 INFO @ Thu, 09 Dec 2021 03:02:49: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:02:49: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:02:49: #1 total tags in treatment: 3700191 INFO @ Thu, 09 Dec 2021 03:02:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:02:49: #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 03:02:49: #1 tags after filtering in treatment: 3341172 INFO @ Thu, 09 Dec 2021 03:02:49: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:02:49: #1 finished! INFO @ Thu, 09 Dec 2021 03:02:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:02:49: #2 number of paired peaks: 734 WARNING @ Thu, 09 Dec 2021 03:02:49: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Thu, 09 Dec 2021 03:02:49: start model_add_line... INFO @ Thu, 09 Dec 2021 03:02:49: start X-correlation... INFO @ Thu, 09 Dec 2021 03:02:49: end of X-cor INFO @ Thu, 09 Dec 2021 03:02:49: #2 finished! INFO @ Thu, 09 Dec 2021 03:02:49: #2 predicted fragment length is 227 bps INFO @ Thu, 09 Dec 2021 03:02:49: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 09 Dec 2021 03:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.10_model.r WARNING @ Thu, 09 Dec 2021 03:02:49: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:02:49: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Thu, 09 Dec 2021 03:02:49: #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 03:02:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:02:52: 9000000 INFO @ Thu, 09 Dec 2021 03:02:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.10_summits.bed INFO @ Thu, 09 Dec 2021 03:03:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:03:03: 10000000 INFO @ Thu, 09 Dec 2021 03:03:14: 11000000 INFO @ Thu, 09 Dec 2021 03:03:24: 12000000 INFO @ Thu, 09 Dec 2021 03:03:24: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:03:24: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:03:24: #1 total tags in treatment: 3700191 INFO @ Thu, 09 Dec 2021 03:03:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:03:24: #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 03:03:25: #1 tags after filtering in treatment: 3341172 INFO @ Thu, 09 Dec 2021 03:03:25: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:03:25: #1 finished! INFO @ Thu, 09 Dec 2021 03:03:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:03:25: #2 number of paired peaks: 734 WARNING @ Thu, 09 Dec 2021 03:03:25: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Thu, 09 Dec 2021 03:03:25: start model_add_line... INFO @ Thu, 09 Dec 2021 03:03:25: start X-correlation... INFO @ Thu, 09 Dec 2021 03:03:25: end of X-cor INFO @ Thu, 09 Dec 2021 03:03:25: #2 finished! INFO @ Thu, 09 Dec 2021 03:03:25: #2 predicted fragment length is 227 bps INFO @ Thu, 09 Dec 2021 03:03:25: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 09 Dec 2021 03:03:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.20_model.r WARNING @ Thu, 09 Dec 2021 03:03:25: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:03:25: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Thu, 09 Dec 2021 03:03:25: #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 03:03:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:03:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:03:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:03:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:03:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:03:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567186/SRX9567186.20_summits.bed INFO @ Thu, 09 Dec 2021 03:03:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (235 records, 4 fields): 2 millis CompletedMACS2peakCalling