Job ID = 14160459 SRX = SRX9904328 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14880659 spots for SRR13491814/SRR13491814.sra Written 14880659 spots for SRR13491814/SRR13491814.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160598 ("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: 00:03:04 14880659 reads; of these: 14880659 (100.00%) were unpaired; of these: 3190440 (21.44%) aligned 0 times 9782804 (65.74%) aligned exactly 1 time 1907415 (12.82%) aligned >1 times 78.56% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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 8 files... [bam_rmdupse_core] 1131990 / 11690219 = 0.0968 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 02:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.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 02:45:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:45:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:45:44: 1000000 INFO @ Thu, 09 Dec 2021 02:45:50: 2000000 INFO @ Thu, 09 Dec 2021 02:45:57: 3000000 INFO @ Thu, 09 Dec 2021 02:46:03: 4000000 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 02:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.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 02:46:08: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:46:08: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:46:10: 5000000 INFO @ Thu, 09 Dec 2021 02:46:14: 1000000 INFO @ Thu, 09 Dec 2021 02:46:17: 6000000 INFO @ Thu, 09 Dec 2021 02:46:21: 2000000 INFO @ Thu, 09 Dec 2021 02:46:24: 7000000 INFO @ Thu, 09 Dec 2021 02:46:27: 3000000 INFO @ Thu, 09 Dec 2021 02:46:31: 8000000 INFO @ Thu, 09 Dec 2021 02:46:33: 4000000 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 02:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.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 02:46:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:46:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:46:38: 9000000 INFO @ Thu, 09 Dec 2021 02:46:39: 5000000 INFO @ Thu, 09 Dec 2021 02:46:44: 1000000 INFO @ Thu, 09 Dec 2021 02:46:45: 10000000 INFO @ Thu, 09 Dec 2021 02:46:45: 6000000 INFO @ Thu, 09 Dec 2021 02:46:49: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:46:49: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:46:49: #1 total tags in treatment: 10558229 INFO @ Thu, 09 Dec 2021 02:46:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:46:49: #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 02:46:49: #1 tags after filtering in treatment: 10558229 INFO @ Thu, 09 Dec 2021 02:46:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:46:49: #1 finished! INFO @ Thu, 09 Dec 2021 02:46:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:46:50: #2 number of paired peaks: 297 WARNING @ Thu, 09 Dec 2021 02:46:50: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Thu, 09 Dec 2021 02:46:50: start model_add_line... INFO @ Thu, 09 Dec 2021 02:46:50: start X-correlation... INFO @ Thu, 09 Dec 2021 02:46:50: end of X-cor INFO @ Thu, 09 Dec 2021 02:46:50: #2 finished! INFO @ Thu, 09 Dec 2021 02:46:50: #2 predicted fragment length is 49 bps INFO @ Thu, 09 Dec 2021 02:46:50: #2 alternative fragment length(s) may be 2,49,526,548 bps INFO @ Thu, 09 Dec 2021 02:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.05_model.r WARNING @ Thu, 09 Dec 2021 02:46:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:46:50: #2 You may need to consider one of the other alternative d(s): 2,49,526,548 WARNING @ Thu, 09 Dec 2021 02:46:50: #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 02:46:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:46:50: 2000000 INFO @ Thu, 09 Dec 2021 02:46:52: 7000000 INFO @ Thu, 09 Dec 2021 02:46:56: 3000000 INFO @ Thu, 09 Dec 2021 02:46:58: 8000000 INFO @ Thu, 09 Dec 2021 02:47:02: 4000000 INFO @ Thu, 09 Dec 2021 02:47:04: 9000000 INFO @ Thu, 09 Dec 2021 02:47:08: 5000000 INFO @ Thu, 09 Dec 2021 02:47:09: 10000000 INFO @ Thu, 09 Dec 2021 02:47:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:47:13: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:47:13: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:47:13: #1 total tags in treatment: 10558229 INFO @ Thu, 09 Dec 2021 02:47:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:47:13: #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 02:47:13: #1 tags after filtering in treatment: 10558229 INFO @ Thu, 09 Dec 2021 02:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:47:13: #1 finished! INFO @ Thu, 09 Dec 2021 02:47:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:47:14: #2 number of paired peaks: 297 WARNING @ Thu, 09 Dec 2021 02:47:14: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Thu, 09 Dec 2021 02:47:14: start model_add_line... INFO @ Thu, 09 Dec 2021 02:47:14: start X-correlation... INFO @ Thu, 09 Dec 2021 02:47:14: end of X-cor INFO @ Thu, 09 Dec 2021 02:47:14: #2 finished! INFO @ Thu, 09 Dec 2021 02:47:14: #2 predicted fragment length is 49 bps INFO @ Thu, 09 Dec 2021 02:47:14: #2 alternative fragment length(s) may be 2,49,526,548 bps INFO @ Thu, 09 Dec 2021 02:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.10_model.r WARNING @ Thu, 09 Dec 2021 02:47:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:47:14: #2 You may need to consider one of the other alternative d(s): 2,49,526,548 WARNING @ Thu, 09 Dec 2021 02:47:14: #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 02:47:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:47:14: 6000000 INFO @ Thu, 09 Dec 2021 02:47:20: 7000000 INFO @ Thu, 09 Dec 2021 02:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.05_summits.bed INFO @ Thu, 09 Dec 2021 02:47:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:47:26: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:47:31: 9000000 INFO @ Thu, 09 Dec 2021 02:47:35: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:47:36: 10000000 INFO @ Thu, 09 Dec 2021 02:47:40: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:47:40: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:47:40: #1 total tags in treatment: 10558229 INFO @ Thu, 09 Dec 2021 02:47:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:47:40: #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 02:47:40: #1 tags after filtering in treatment: 10558229 INFO @ Thu, 09 Dec 2021 02:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:47:40: #1 finished! INFO @ Thu, 09 Dec 2021 02:47:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:47:40: #2 number of paired peaks: 297 WARNING @ Thu, 09 Dec 2021 02:47:40: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Thu, 09 Dec 2021 02:47:40: start model_add_line... INFO @ Thu, 09 Dec 2021 02:47:40: start X-correlation... INFO @ Thu, 09 Dec 2021 02:47:40: end of X-cor INFO @ Thu, 09 Dec 2021 02:47:40: #2 finished! INFO @ Thu, 09 Dec 2021 02:47:40: #2 predicted fragment length is 49 bps INFO @ Thu, 09 Dec 2021 02:47:40: #2 alternative fragment length(s) may be 2,49,526,548 bps INFO @ Thu, 09 Dec 2021 02:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.20_model.r WARNING @ Thu, 09 Dec 2021 02:47:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:47:41: #2 You may need to consider one of the other alternative d(s): 2,49,526,548 WARNING @ Thu, 09 Dec 2021 02:47:41: #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 02:47:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.10_summits.bed INFO @ Thu, 09 Dec 2021 02:47:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (430 records, 4 fields): 75 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:48:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904328/SRX9904328.20_summits.bed INFO @ Thu, 09 Dec 2021 02:48:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling