Job ID = 6626428 SRX = SRX7630547 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31885727 spots for SRR10964909/SRR10964909.sra Written 31885727 spots for SRR10964909/SRR10964909.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626602 ("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: 00:05:36 31885727 reads; of these: 31885727 (100.00%) were unpaired; of these: 10816465 (33.92%) aligned 0 times 17606117 (55.22%) aligned exactly 1 time 3463145 (10.86%) aligned >1 times 66.08% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 7932212 / 21069262 = 0.3765 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.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 @ Tue, 14 Jul 2020 07:12:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:12:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:12:11: 1000000 INFO @ Tue, 14 Jul 2020 07:12:16: 2000000 INFO @ Tue, 14 Jul 2020 07:12:21: 3000000 INFO @ Tue, 14 Jul 2020 07:12:26: 4000000 INFO @ Tue, 14 Jul 2020 07:12:31: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:12:36: 6000000 INFO @ Tue, 14 Jul 2020 07:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.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 @ Tue, 14 Jul 2020 07:12:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:12:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:12:41: 7000000 INFO @ Tue, 14 Jul 2020 07:12:42: 1000000 INFO @ Tue, 14 Jul 2020 07:12:46: 8000000 INFO @ Tue, 14 Jul 2020 07:12:49: 2000000 INFO @ Tue, 14 Jul 2020 07:12:51: 9000000 INFO @ Tue, 14 Jul 2020 07:12:56: 3000000 INFO @ Tue, 14 Jul 2020 07:12:56: 10000000 INFO @ Tue, 14 Jul 2020 07:13:01: 11000000 INFO @ Tue, 14 Jul 2020 07:13:03: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.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 @ Tue, 14 Jul 2020 07:13:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:13:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:13:06: 12000000 INFO @ Tue, 14 Jul 2020 07:13:10: 5000000 INFO @ Tue, 14 Jul 2020 07:13:11: 1000000 INFO @ Tue, 14 Jul 2020 07:13:11: 13000000 INFO @ Tue, 14 Jul 2020 07:13:12: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:13:12: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:13:12: #1 total tags in treatment: 13137050 INFO @ Tue, 14 Jul 2020 07:13:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:13:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:13:12: #1 tags after filtering in treatment: 13137050 INFO @ Tue, 14 Jul 2020 07:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:13:12: #1 finished! INFO @ Tue, 14 Jul 2020 07:13:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:13:13: #2 number of paired peaks: 326 WARNING @ Tue, 14 Jul 2020 07:13:13: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 14 Jul 2020 07:13:13: start model_add_line... INFO @ Tue, 14 Jul 2020 07:13:13: start X-correlation... INFO @ Tue, 14 Jul 2020 07:13:13: end of X-cor INFO @ Tue, 14 Jul 2020 07:13:13: #2 finished! INFO @ Tue, 14 Jul 2020 07:13:13: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 07:13:13: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 14 Jul 2020 07:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.05_model.r WARNING @ Tue, 14 Jul 2020 07:13:13: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:13:13: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 14 Jul 2020 07:13:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:13:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:13:17: 2000000 INFO @ Tue, 14 Jul 2020 07:13:17: 6000000 INFO @ Tue, 14 Jul 2020 07:13:22: 3000000 INFO @ Tue, 14 Jul 2020 07:13:24: 7000000 INFO @ Tue, 14 Jul 2020 07:13:27: 4000000 INFO @ Tue, 14 Jul 2020 07:13:30: 8000000 INFO @ Tue, 14 Jul 2020 07:13:32: 5000000 INFO @ Tue, 14 Jul 2020 07:13:35: 9000000 INFO @ Tue, 14 Jul 2020 07:13:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:13:37: 6000000 INFO @ Tue, 14 Jul 2020 07:13:40: 10000000 INFO @ Tue, 14 Jul 2020 07:13:42: 7000000 INFO @ Tue, 14 Jul 2020 07:13:46: 11000000 INFO @ Tue, 14 Jul 2020 07:13:47: 8000000 INFO @ Tue, 14 Jul 2020 07:13:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:13:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:13:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.05_summits.bed INFO @ Tue, 14 Jul 2020 07:13:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:13:51: 12000000 INFO @ Tue, 14 Jul 2020 07:13:53: 9000000 INFO @ Tue, 14 Jul 2020 07:13:56: 13000000 INFO @ Tue, 14 Jul 2020 07:13:57: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:13:57: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:13:57: #1 total tags in treatment: 13137050 INFO @ Tue, 14 Jul 2020 07:13:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:13:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:13:57: #1 tags after filtering in treatment: 13137050 INFO @ Tue, 14 Jul 2020 07:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:13:57: #1 finished! INFO @ Tue, 14 Jul 2020 07:13:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:13:58: 10000000 INFO @ Tue, 14 Jul 2020 07:13:58: #2 number of paired peaks: 326 WARNING @ Tue, 14 Jul 2020 07:13:58: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 14 Jul 2020 07:13:58: start model_add_line... INFO @ Tue, 14 Jul 2020 07:13:58: start X-correlation... INFO @ Tue, 14 Jul 2020 07:13:58: end of X-cor INFO @ Tue, 14 Jul 2020 07:13:58: #2 finished! INFO @ Tue, 14 Jul 2020 07:13:58: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 07:13:58: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 14 Jul 2020 07:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.10_model.r WARNING @ Tue, 14 Jul 2020 07:13:58: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:13:58: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 14 Jul 2020 07:13:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:13:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:14:03: 11000000 INFO @ Tue, 14 Jul 2020 07:14:08: 12000000 INFO @ Tue, 14 Jul 2020 07:14:13: 13000000 INFO @ Tue, 14 Jul 2020 07:14:14: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:14:14: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:14:14: #1 total tags in treatment: 13137050 INFO @ Tue, 14 Jul 2020 07:14:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:14:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:14:14: #1 tags after filtering in treatment: 13137050 INFO @ Tue, 14 Jul 2020 07:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:14:14: #1 finished! INFO @ Tue, 14 Jul 2020 07:14:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:14:15: #2 number of paired peaks: 326 WARNING @ Tue, 14 Jul 2020 07:14:15: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 14 Jul 2020 07:14:15: start model_add_line... INFO @ Tue, 14 Jul 2020 07:14:15: start X-correlation... INFO @ Tue, 14 Jul 2020 07:14:15: end of X-cor INFO @ Tue, 14 Jul 2020 07:14:15: #2 finished! INFO @ Tue, 14 Jul 2020 07:14:15: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 07:14:15: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 14 Jul 2020 07:14:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.20_model.r WARNING @ Tue, 14 Jul 2020 07:14:15: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:14:15: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 14 Jul 2020 07:14:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:14:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:14:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:14:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.10_summits.bed INFO @ Tue, 14 Jul 2020 07:14:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:14:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630547/SRX7630547.20_summits.bed INFO @ Tue, 14 Jul 2020 07:14:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling