Job ID = 14158114 SRX = SRX7739516 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14060602 spots for SRR11100920/SRR11100920.sra Written 14060602 spots for SRR11100920/SRR11100920.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158374 ("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: 00:03:17 14060602 reads; of these: 14060602 (100.00%) were unpaired; of these: 1505134 (10.70%) aligned 0 times 10525305 (74.86%) aligned exactly 1 time 2030163 (14.44%) aligned >1 times 89.30% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 3750970 / 12555468 = 0.2988 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 14:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.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 14:32:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:53: 1000000 INFO @ Wed, 08 Dec 2021 14:32:59: 2000000 INFO @ Wed, 08 Dec 2021 14:33:06: 3000000 INFO @ Wed, 08 Dec 2021 14:33:13: 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 @ Wed, 08 Dec 2021 14:33:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.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 14:33:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:33:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:33:20: 5000000 INFO @ Wed, 08 Dec 2021 14:33:22: 1000000 INFO @ Wed, 08 Dec 2021 14:33:27: 6000000 INFO @ Wed, 08 Dec 2021 14:33:29: 2000000 INFO @ Wed, 08 Dec 2021 14:33:35: 7000000 INFO @ Wed, 08 Dec 2021 14:33:36: 3000000 INFO @ Wed, 08 Dec 2021 14:33:42: 4000000 INFO @ Wed, 08 Dec 2021 14:33:43: 8000000 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 14:33:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.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 14:33:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:33:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:33:49: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:33:49: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:33:49: #1 total tags in treatment: 8804498 INFO @ Wed, 08 Dec 2021 14:33:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:33:49: #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 14:33:49: 5000000 INFO @ Wed, 08 Dec 2021 14:33:49: #1 tags after filtering in treatment: 8804498 INFO @ Wed, 08 Dec 2021 14:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:33:49: #1 finished! INFO @ Wed, 08 Dec 2021 14:33:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:33:50: #2 number of paired peaks: 401 WARNING @ Wed, 08 Dec 2021 14:33:50: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Wed, 08 Dec 2021 14:33:50: start model_add_line... INFO @ Wed, 08 Dec 2021 14:33:50: start X-correlation... INFO @ Wed, 08 Dec 2021 14:33:50: end of X-cor INFO @ Wed, 08 Dec 2021 14:33:50: #2 finished! INFO @ Wed, 08 Dec 2021 14:33:50: #2 predicted fragment length is 53 bps INFO @ Wed, 08 Dec 2021 14:33:50: #2 alternative fragment length(s) may be 3,53,595 bps INFO @ Wed, 08 Dec 2021 14:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.05_model.r WARNING @ Wed, 08 Dec 2021 14:33:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:33:50: #2 You may need to consider one of the other alternative d(s): 3,53,595 WARNING @ Wed, 08 Dec 2021 14:33:50: #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 14:33:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:33:53: 1000000 INFO @ Wed, 08 Dec 2021 14:33:56: 6000000 INFO @ Wed, 08 Dec 2021 14:34:00: 2000000 INFO @ Wed, 08 Dec 2021 14:34:02: 7000000 INFO @ Wed, 08 Dec 2021 14:34:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:34:07: 3000000 INFO @ Wed, 08 Dec 2021 14:34:09: 8000000 INFO @ Wed, 08 Dec 2021 14:34:14: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:34:14: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:34:14: #1 total tags in treatment: 8804498 INFO @ Wed, 08 Dec 2021 14:34:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:34:14: #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 14:34:14: 4000000 INFO @ Wed, 08 Dec 2021 14:34:15: #1 tags after filtering in treatment: 8804498 INFO @ Wed, 08 Dec 2021 14:34:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:34:15: #1 finished! INFO @ Wed, 08 Dec 2021 14:34:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:34:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.05_summits.bed INFO @ Wed, 08 Dec 2021 14:34:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (791 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:34:15: #2 number of paired peaks: 401 WARNING @ Wed, 08 Dec 2021 14:34:15: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Wed, 08 Dec 2021 14:34:15: start model_add_line... INFO @ Wed, 08 Dec 2021 14:34:15: start X-correlation... INFO @ Wed, 08 Dec 2021 14:34:15: end of X-cor INFO @ Wed, 08 Dec 2021 14:34:15: #2 finished! INFO @ Wed, 08 Dec 2021 14:34:15: #2 predicted fragment length is 53 bps INFO @ Wed, 08 Dec 2021 14:34:15: #2 alternative fragment length(s) may be 3,53,595 bps INFO @ Wed, 08 Dec 2021 14:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.10_model.r WARNING @ Wed, 08 Dec 2021 14:34:15: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:34:15: #2 You may need to consider one of the other alternative d(s): 3,53,595 WARNING @ Wed, 08 Dec 2021 14:34:15: #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 14:34:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:34:21: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:34:28: 6000000 INFO @ Wed, 08 Dec 2021 14:34:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:34:34: 7000000 INFO @ Wed, 08 Dec 2021 14:34:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:34:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:34:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.10_summits.bed INFO @ Wed, 08 Dec 2021 14:34:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 144 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:34:41: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:34:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:34:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:34:46: #1 total tags in treatment: 8804498 INFO @ Wed, 08 Dec 2021 14:34:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:34:46: #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 14:34:46: #1 tags after filtering in treatment: 8804498 INFO @ Wed, 08 Dec 2021 14:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:34:46: #1 finished! INFO @ Wed, 08 Dec 2021 14:34:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:34:46: #2 number of paired peaks: 401 WARNING @ Wed, 08 Dec 2021 14:34:46: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Wed, 08 Dec 2021 14:34:46: start model_add_line... INFO @ Wed, 08 Dec 2021 14:34:47: start X-correlation... INFO @ Wed, 08 Dec 2021 14:34:47: end of X-cor INFO @ Wed, 08 Dec 2021 14:34:47: #2 finished! INFO @ Wed, 08 Dec 2021 14:34:47: #2 predicted fragment length is 53 bps INFO @ Wed, 08 Dec 2021 14:34:47: #2 alternative fragment length(s) may be 3,53,595 bps INFO @ Wed, 08 Dec 2021 14:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.20_model.r WARNING @ Wed, 08 Dec 2021 14:34:47: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:34:47: #2 You may need to consider one of the other alternative d(s): 3,53,595 WARNING @ Wed, 08 Dec 2021 14:34:47: #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 14:34:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:35:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:35:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:35:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739516/SRX7739516.20_summits.bed INFO @ Wed, 08 Dec 2021 14:35:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (202 records, 4 fields): 2 millis CompletedMACS2peakCalling