Job ID = 14158369 SRX = SRX7665450 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14213636 spots for SRR11004634/SRR11004634.sra Written 14213636 spots for SRR11004634/SRR11004634.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158898 ("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: 00:02:58 14213636 reads; of these: 14213636 (100.00%) were unpaired; of these: 544797 (3.83%) aligned 0 times 11628393 (81.81%) aligned exactly 1 time 2040446 (14.36%) aligned >1 times 96.17% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 1510197 / 13668839 = 0.1105 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 @ Wed, 08 Dec 2021 16:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.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 @ Wed, 08 Dec 2021 16:28:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:28:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:28:38: 1000000 INFO @ Wed, 08 Dec 2021 16:28:42: 2000000 INFO @ Wed, 08 Dec 2021 16:28:47: 3000000 INFO @ Wed, 08 Dec 2021 16:28:51: 4000000 INFO @ Wed, 08 Dec 2021 16:28:56: 5000000 INFO @ Wed, 08 Dec 2021 16:29:00: 6000000 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 @ Wed, 08 Dec 2021 16:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.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 @ Wed, 08 Dec 2021 16:29:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:29:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:29:04: 7000000 INFO @ Wed, 08 Dec 2021 16:29:09: 8000000 INFO @ Wed, 08 Dec 2021 16:29:09: 1000000 INFO @ Wed, 08 Dec 2021 16:29:13: 9000000 INFO @ Wed, 08 Dec 2021 16:29:14: 2000000 INFO @ Wed, 08 Dec 2021 16:29:18: 10000000 INFO @ Wed, 08 Dec 2021 16:29:19: 3000000 INFO @ Wed, 08 Dec 2021 16:29:22: 11000000 INFO @ Wed, 08 Dec 2021 16:29:24: 4000000 INFO @ Wed, 08 Dec 2021 16:29:27: 12000000 INFO @ Wed, 08 Dec 2021 16:29:28: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 16:29:28: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 16:29:28: #1 total tags in treatment: 12158642 INFO @ Wed, 08 Dec 2021 16:29:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:29:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:29:28: #1 tags after filtering in treatment: 12158642 INFO @ Wed, 08 Dec 2021 16:29:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:29:28: #1 finished! INFO @ Wed, 08 Dec 2021 16:29:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:29:29: #2 number of paired peaks: 214 WARNING @ Wed, 08 Dec 2021 16:29:29: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Wed, 08 Dec 2021 16:29:29: start model_add_line... INFO @ Wed, 08 Dec 2021 16:29:29: start X-correlation... INFO @ Wed, 08 Dec 2021 16:29:29: end of X-cor INFO @ Wed, 08 Dec 2021 16:29:29: #2 finished! INFO @ Wed, 08 Dec 2021 16:29:29: #2 predicted fragment length is 57 bps INFO @ Wed, 08 Dec 2021 16:29:29: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 08 Dec 2021 16:29:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.05_model.r WARNING @ Wed, 08 Dec 2021 16:29:29: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:29:29: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Wed, 08 Dec 2021 16:29:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:29:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:29:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:29:29: 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 @ Wed, 08 Dec 2021 16:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.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 @ Wed, 08 Dec 2021 16:29:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:29:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:29:34: 6000000 INFO @ Wed, 08 Dec 2021 16:29:39: 1000000 INFO @ Wed, 08 Dec 2021 16:29:39: 7000000 INFO @ Wed, 08 Dec 2021 16:29:44: 2000000 INFO @ Wed, 08 Dec 2021 16:29:44: 8000000 INFO @ Wed, 08 Dec 2021 16:29:49: 3000000 INFO @ Wed, 08 Dec 2021 16:29:49: 9000000 INFO @ Wed, 08 Dec 2021 16:29:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:29:54: 4000000 INFO @ Wed, 08 Dec 2021 16:29:55: 10000000 INFO @ Wed, 08 Dec 2021 16:29:59: 5000000 INFO @ Wed, 08 Dec 2021 16:30:00: 11000000 INFO @ Wed, 08 Dec 2021 16:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.05_summits.bed INFO @ Wed, 08 Dec 2021 16:30:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4322 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:30:04: 6000000 INFO @ Wed, 08 Dec 2021 16:30:05: 12000000 INFO @ Wed, 08 Dec 2021 16:30:05: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 16:30:05: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 16:30:05: #1 total tags in treatment: 12158642 INFO @ Wed, 08 Dec 2021 16:30:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:30:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:30:06: #1 tags after filtering in treatment: 12158642 INFO @ Wed, 08 Dec 2021 16:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:30:06: #1 finished! INFO @ Wed, 08 Dec 2021 16:30:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:30:06: #2 number of paired peaks: 214 WARNING @ Wed, 08 Dec 2021 16:30:06: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Wed, 08 Dec 2021 16:30:06: start model_add_line... INFO @ Wed, 08 Dec 2021 16:30:07: start X-correlation... INFO @ Wed, 08 Dec 2021 16:30:07: end of X-cor INFO @ Wed, 08 Dec 2021 16:30:07: #2 finished! INFO @ Wed, 08 Dec 2021 16:30:07: #2 predicted fragment length is 57 bps INFO @ Wed, 08 Dec 2021 16:30:07: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 08 Dec 2021 16:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.10_model.r WARNING @ Wed, 08 Dec 2021 16:30:07: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:30:07: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Wed, 08 Dec 2021 16:30:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:30:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:30:09: 7000000 INFO @ Wed, 08 Dec 2021 16:30:14: 8000000 INFO @ Wed, 08 Dec 2021 16:30:19: 9000000 INFO @ Wed, 08 Dec 2021 16:30:24: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:30:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:30:29: 11000000 INFO @ Wed, 08 Dec 2021 16:30:34: 12000000 INFO @ Wed, 08 Dec 2021 16:30:35: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 16:30:35: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 16:30:35: #1 total tags in treatment: 12158642 INFO @ Wed, 08 Dec 2021 16:30:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:30:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:30:36: #1 tags after filtering in treatment: 12158642 INFO @ Wed, 08 Dec 2021 16:30:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:30:36: #1 finished! INFO @ Wed, 08 Dec 2021 16:30:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:30:36: #2 number of paired peaks: 214 WARNING @ Wed, 08 Dec 2021 16:30:36: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Wed, 08 Dec 2021 16:30:36: start model_add_line... INFO @ Wed, 08 Dec 2021 16:30:36: start X-correlation... INFO @ Wed, 08 Dec 2021 16:30:36: end of X-cor INFO @ Wed, 08 Dec 2021 16:30:36: #2 finished! INFO @ Wed, 08 Dec 2021 16:30:36: #2 predicted fragment length is 57 bps INFO @ Wed, 08 Dec 2021 16:30:36: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 08 Dec 2021 16:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.20_model.r WARNING @ Wed, 08 Dec 2021 16:30:36: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:30:36: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Wed, 08 Dec 2021 16:30:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:30:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.10_summits.bed INFO @ Wed, 08 Dec 2021 16:30:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1287 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:30:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7665450/SRX7665450.20_summits.bed INFO @ Wed, 08 Dec 2021 16:31:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (293 records, 4 fields): 2 millis CompletedMACS2peakCalling