Job ID = 14159689 SRX = SRX8845627 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:34 7092227 reads; of these: 7092227 (100.00%) were paired; of these: 2336606 (32.95%) aligned concordantly 0 times 4197554 (59.19%) aligned concordantly exactly 1 time 558067 (7.87%) aligned concordantly >1 times ---- 2336606 pairs aligned concordantly 0 times; of these: 864929 (37.02%) aligned discordantly 1 time ---- 1471677 pairs aligned 0 times concordantly or discordantly; of these: 2943354 mates make up the pairs; of these: 2505517 (85.12%) aligned 0 times 234683 (7.97%) aligned exactly 1 time 203154 (6.90%) aligned >1 times 82.34% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 785746 / 5568152 = 0.1411 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 00:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.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 00:31:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:31:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:31:13: 1000000 INFO @ Thu, 09 Dec 2021 00:31:19: 2000000 INFO @ Thu, 09 Dec 2021 00:31:24: 3000000 INFO @ Thu, 09 Dec 2021 00:31:30: 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 00:31:35: 5000000 INFO @ Thu, 09 Dec 2021 00:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.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 00:31:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:31:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:31:41: 6000000 INFO @ Thu, 09 Dec 2021 00:31:43: 1000000 INFO @ Thu, 09 Dec 2021 00:31:47: 7000000 INFO @ Thu, 09 Dec 2021 00:31:49: 2000000 INFO @ Thu, 09 Dec 2021 00:31:53: 8000000 INFO @ Thu, 09 Dec 2021 00:31:55: 3000000 INFO @ Thu, 09 Dec 2021 00:32:00: 9000000 INFO @ Thu, 09 Dec 2021 00:32:01: 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 00:32:06: 10000000 INFO @ Thu, 09 Dec 2021 00:32:06: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:32:06: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:32:06: #1 total tags in treatment: 4098860 INFO @ Thu, 09 Dec 2021 00:32:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:32:06: #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 00:32:06: #1 tags after filtering in treatment: 3072872 INFO @ Thu, 09 Dec 2021 00:32:06: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 09 Dec 2021 00:32:06: #1 finished! INFO @ Thu, 09 Dec 2021 00:32:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:32:07: #2 number of paired peaks: 2997 INFO @ Thu, 09 Dec 2021 00:32:07: start model_add_line... INFO @ Thu, 09 Dec 2021 00:32:07: start X-correlation... INFO @ Thu, 09 Dec 2021 00:32:07: end of X-cor INFO @ Thu, 09 Dec 2021 00:32:07: #2 finished! INFO @ Thu, 09 Dec 2021 00:32:07: #2 predicted fragment length is 111 bps INFO @ Thu, 09 Dec 2021 00:32:07: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 09 Dec 2021 00:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.05_model.r WARNING @ Thu, 09 Dec 2021 00:32:07: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:32:07: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Thu, 09 Dec 2021 00:32:07: #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 00:32:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.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 00:32:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:32:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:32:07: 5000000 INFO @ Thu, 09 Dec 2021 00:32:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:32:14: 6000000 INFO @ Thu, 09 Dec 2021 00:32:14: 1000000 INFO @ Thu, 09 Dec 2021 00:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.05_summits.bed INFO @ Thu, 09 Dec 2021 00:32:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7013 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:32:20: 7000000 INFO @ Thu, 09 Dec 2021 00:32:22: 2000000 INFO @ Thu, 09 Dec 2021 00:32:27: 8000000 INFO @ Thu, 09 Dec 2021 00:32:29: 3000000 INFO @ Thu, 09 Dec 2021 00:32:33: 9000000 INFO @ Thu, 09 Dec 2021 00:32:37: 4000000 INFO @ Thu, 09 Dec 2021 00:32:40: 10000000 INFO @ Thu, 09 Dec 2021 00:32:41: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:32:41: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:32:41: #1 total tags in treatment: 4098860 INFO @ Thu, 09 Dec 2021 00:32:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:32:41: #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 00:32:41: #1 tags after filtering in treatment: 3072872 INFO @ Thu, 09 Dec 2021 00:32:41: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 09 Dec 2021 00:32:41: #1 finished! INFO @ Thu, 09 Dec 2021 00:32:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:32:41: #2 number of paired peaks: 2997 INFO @ Thu, 09 Dec 2021 00:32:41: start model_add_line... INFO @ Thu, 09 Dec 2021 00:32:41: start X-correlation... INFO @ Thu, 09 Dec 2021 00:32:41: end of X-cor INFO @ Thu, 09 Dec 2021 00:32:41: #2 finished! INFO @ Thu, 09 Dec 2021 00:32:41: #2 predicted fragment length is 111 bps INFO @ Thu, 09 Dec 2021 00:32:41: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 09 Dec 2021 00:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.10_model.r WARNING @ Thu, 09 Dec 2021 00:32:41: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:32:41: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Thu, 09 Dec 2021 00:32:41: #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 00:32:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:32:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:32:48: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.10_summits.bed INFO @ Thu, 09 Dec 2021 00:32:51: Done! INFO @ Thu, 09 Dec 2021 00:32:51: 6000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4551 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:32:58: 7000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:33:05: 8000000 INFO @ Thu, 09 Dec 2021 00:33:12: 9000000 INFO @ Thu, 09 Dec 2021 00:33:19: 10000000 INFO @ Thu, 09 Dec 2021 00:33:19: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:33:19: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:33:19: #1 total tags in treatment: 4098860 INFO @ Thu, 09 Dec 2021 00:33:19: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:33:19: #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 00:33:19: #1 tags after filtering in treatment: 3072872 INFO @ Thu, 09 Dec 2021 00:33:19: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 09 Dec 2021 00:33:19: #1 finished! INFO @ Thu, 09 Dec 2021 00:33:19: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:33:20: #2 number of paired peaks: 2997 INFO @ Thu, 09 Dec 2021 00:33:20: start model_add_line... INFO @ Thu, 09 Dec 2021 00:33:20: start X-correlation... INFO @ Thu, 09 Dec 2021 00:33:20: end of X-cor INFO @ Thu, 09 Dec 2021 00:33:20: #2 finished! INFO @ Thu, 09 Dec 2021 00:33:20: #2 predicted fragment length is 111 bps INFO @ Thu, 09 Dec 2021 00:33:20: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 09 Dec 2021 00:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.20_model.r WARNING @ Thu, 09 Dec 2021 00:33:20: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:33:20: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Thu, 09 Dec 2021 00:33:20: #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 00:33:20: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:33:27: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845627/SRX8845627.20_summits.bed INFO @ Thu, 09 Dec 2021 00:33:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 4 millis CompletedMACS2peakCalling