Job ID = 14160421 SRX = SRX8151890 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21665093 spots for SRR11584268/SRR11584268.sra Written 21665093 spots for SRR11584268/SRR11584268.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160552 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:56 21665093 reads; of these: 21665093 (100.00%) were unpaired; of these: 1611405 (7.44%) aligned 0 times 16739115 (77.26%) aligned exactly 1 time 3314573 (15.30%) aligned >1 times 92.56% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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 12 files... [bam_rmdupse_core] 1841735 / 20053688 = 0.0918 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 02:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.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 02:29:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:29:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:29:33: 1000000 INFO @ Thu, 09 Dec 2021 02:29:38: 2000000 INFO @ Thu, 09 Dec 2021 02:29:43: 3000000 INFO @ Thu, 09 Dec 2021 02:29:48: 4000000 INFO @ Thu, 09 Dec 2021 02:29:53: 5000000 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 02:29:58: 6000000 INFO @ Thu, 09 Dec 2021 02:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.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 02:29:58: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:29:58: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:30:03: 7000000 INFO @ Thu, 09 Dec 2021 02:30:03: 1000000 INFO @ Thu, 09 Dec 2021 02:30:08: 8000000 INFO @ Thu, 09 Dec 2021 02:30:09: 2000000 INFO @ Thu, 09 Dec 2021 02:30:14: 9000000 INFO @ Thu, 09 Dec 2021 02:30:14: 3000000 INFO @ Thu, 09 Dec 2021 02:30:19: 10000000 INFO @ Thu, 09 Dec 2021 02:30:20: 4000000 INFO @ Thu, 09 Dec 2021 02:30:24: 11000000 INFO @ Thu, 09 Dec 2021 02:30:25: 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 02:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.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 02:30:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:30:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:30:30: 12000000 INFO @ Thu, 09 Dec 2021 02:30:31: 6000000 INFO @ Thu, 09 Dec 2021 02:30:33: 1000000 INFO @ Thu, 09 Dec 2021 02:30:35: 13000000 INFO @ Thu, 09 Dec 2021 02:30:36: 7000000 INFO @ Thu, 09 Dec 2021 02:30:39: 2000000 INFO @ Thu, 09 Dec 2021 02:30:41: 14000000 INFO @ Thu, 09 Dec 2021 02:30:42: 8000000 INFO @ Thu, 09 Dec 2021 02:30:44: 3000000 INFO @ Thu, 09 Dec 2021 02:30:46: 15000000 INFO @ Thu, 09 Dec 2021 02:30:47: 9000000 INFO @ Thu, 09 Dec 2021 02:30:50: 4000000 INFO @ Thu, 09 Dec 2021 02:30:52: 16000000 INFO @ Thu, 09 Dec 2021 02:30:53: 10000000 INFO @ Thu, 09 Dec 2021 02:30:55: 5000000 INFO @ Thu, 09 Dec 2021 02:30:57: 17000000 INFO @ Thu, 09 Dec 2021 02:30:58: 11000000 INFO @ Thu, 09 Dec 2021 02:31:01: 6000000 INFO @ Thu, 09 Dec 2021 02:31:02: 18000000 INFO @ Thu, 09 Dec 2021 02:31:04: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:31:04: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:31:04: #1 total tags in treatment: 18211953 INFO @ Thu, 09 Dec 2021 02:31:04: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:31:04: #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 02:31:04: 12000000 INFO @ Thu, 09 Dec 2021 02:31:04: #1 tags after filtering in treatment: 18211953 INFO @ Thu, 09 Dec 2021 02:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:31:04: #1 finished! INFO @ Thu, 09 Dec 2021 02:31:04: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:31:05: #2 number of paired peaks: 206 WARNING @ Thu, 09 Dec 2021 02:31:05: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Thu, 09 Dec 2021 02:31:05: start model_add_line... INFO @ Thu, 09 Dec 2021 02:31:05: start X-correlation... INFO @ Thu, 09 Dec 2021 02:31:05: end of X-cor INFO @ Thu, 09 Dec 2021 02:31:05: #2 finished! INFO @ Thu, 09 Dec 2021 02:31:05: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 02:31:05: #2 alternative fragment length(s) may be 1,10,34,553,567,589 bps INFO @ Thu, 09 Dec 2021 02:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.05_model.r WARNING @ Thu, 09 Dec 2021 02:31:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:31:05: #2 You may need to consider one of the other alternative d(s): 1,10,34,553,567,589 WARNING @ Thu, 09 Dec 2021 02:31:05: #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 02:31:05: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:31:06: 7000000 INFO @ Thu, 09 Dec 2021 02:31:09: 13000000 INFO @ Thu, 09 Dec 2021 02:31:12: 8000000 INFO @ Thu, 09 Dec 2021 02:31:15: 14000000 INFO @ Thu, 09 Dec 2021 02:31:17: 9000000 INFO @ Thu, 09 Dec 2021 02:31:20: 15000000 INFO @ Thu, 09 Dec 2021 02:31:23: 10000000 INFO @ Thu, 09 Dec 2021 02:31:25: 16000000 INFO @ Thu, 09 Dec 2021 02:31:28: 11000000 INFO @ Thu, 09 Dec 2021 02:31:31: 17000000 INFO @ Thu, 09 Dec 2021 02:31:33: 12000000 INFO @ Thu, 09 Dec 2021 02:31:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:31:36: 18000000 INFO @ Thu, 09 Dec 2021 02:31:37: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:31:37: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:31:37: #1 total tags in treatment: 18211953 INFO @ Thu, 09 Dec 2021 02:31:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:31:37: #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 02:31:38: #1 tags after filtering in treatment: 18211953 INFO @ Thu, 09 Dec 2021 02:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:31:38: #1 finished! INFO @ Thu, 09 Dec 2021 02:31:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:31:39: 13000000 INFO @ Thu, 09 Dec 2021 02:31:39: #2 number of paired peaks: 206 WARNING @ Thu, 09 Dec 2021 02:31:39: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Thu, 09 Dec 2021 02:31:39: start model_add_line... INFO @ Thu, 09 Dec 2021 02:31:39: start X-correlation... INFO @ Thu, 09 Dec 2021 02:31:39: end of X-cor INFO @ Thu, 09 Dec 2021 02:31:39: #2 finished! INFO @ Thu, 09 Dec 2021 02:31:39: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 02:31:39: #2 alternative fragment length(s) may be 1,10,34,553,567,589 bps INFO @ Thu, 09 Dec 2021 02:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.10_model.r WARNING @ Thu, 09 Dec 2021 02:31:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:31:39: #2 You may need to consider one of the other alternative d(s): 1,10,34,553,567,589 WARNING @ Thu, 09 Dec 2021 02:31:39: #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 02:31:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:31:44: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.05_summits.bed INFO @ Thu, 09 Dec 2021 02:31:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:31:49: 15000000 INFO @ Thu, 09 Dec 2021 02:31:55: 16000000 INFO @ Thu, 09 Dec 2021 02:32:00: 17000000 INFO @ Thu, 09 Dec 2021 02:32:05: 18000000 INFO @ Thu, 09 Dec 2021 02:32:06: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:32:06: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:32:06: #1 total tags in treatment: 18211953 INFO @ Thu, 09 Dec 2021 02:32:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:32:06: #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 02:32:06: #1 tags after filtering in treatment: 18211953 INFO @ Thu, 09 Dec 2021 02:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:32:06: #1 finished! INFO @ Thu, 09 Dec 2021 02:32:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:32:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:32:08: #2 number of paired peaks: 206 WARNING @ Thu, 09 Dec 2021 02:32:08: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Thu, 09 Dec 2021 02:32:08: start model_add_line... INFO @ Thu, 09 Dec 2021 02:32:08: start X-correlation... INFO @ Thu, 09 Dec 2021 02:32:08: end of X-cor INFO @ Thu, 09 Dec 2021 02:32:08: #2 finished! INFO @ Thu, 09 Dec 2021 02:32:08: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 02:32:08: #2 alternative fragment length(s) may be 1,10,34,553,567,589 bps INFO @ Thu, 09 Dec 2021 02:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.20_model.r WARNING @ Thu, 09 Dec 2021 02:32:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:32:08: #2 You may need to consider one of the other alternative d(s): 1,10,34,553,567,589 WARNING @ Thu, 09 Dec 2021 02:32:08: #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 02:32:08: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.10_summits.bed INFO @ Thu, 09 Dec 2021 02:32:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:32:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8151890/SRX8151890.20_summits.bed INFO @ Thu, 09 Dec 2021 02:32:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling