Job ID = 14160683 SRX = SRX9567170 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: 02:25:53 27040874 reads; of these: 27040874 (100.00%) were paired; of these: 8122028 (30.04%) aligned concordantly 0 times 7958563 (29.43%) aligned concordantly exactly 1 time 10960283 (40.53%) aligned concordantly >1 times ---- 8122028 pairs aligned concordantly 0 times; of these: 4883342 (60.12%) aligned discordantly 1 time ---- 3238686 pairs aligned 0 times concordantly or discordantly; of these: 6477372 mates make up the pairs; of these: 3618683 (55.87%) aligned 0 times 1148355 (17.73%) aligned exactly 1 time 1710334 (26.40%) aligned >1 times 93.31% overall alignment rate Time searching: 02:25:53 Overall time: 02:25:53 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 40 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] 19019692 / 23757421 = 0.8006 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 06:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.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 06:27:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 06:27:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 06:28:08: 1000000 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 06:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.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 06:28:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 06:28:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 06:28:23: 2000000 INFO @ Thu, 09 Dec 2021 06:28:38: 3000000 INFO @ Thu, 09 Dec 2021 06:28:39: 1000000 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 06:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.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 06:28:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 06:28:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 06:28:54: 4000000 INFO @ Thu, 09 Dec 2021 06:28:56: 2000000 INFO @ Thu, 09 Dec 2021 06:29:09: 5000000 INFO @ Thu, 09 Dec 2021 06:29:13: 1000000 INFO @ Thu, 09 Dec 2021 06:29:14: 3000000 INFO @ Thu, 09 Dec 2021 06:29:24: 6000000 INFO @ Thu, 09 Dec 2021 06:29:32: 2000000 INFO @ Thu, 09 Dec 2021 06:29:34: 4000000 INFO @ Thu, 09 Dec 2021 06:29:40: 7000000 INFO @ Thu, 09 Dec 2021 06:29:51: 3000000 INFO @ Thu, 09 Dec 2021 06:29:52: 5000000 INFO @ Thu, 09 Dec 2021 06:29:55: 8000000 INFO @ Thu, 09 Dec 2021 06:30:09: 6000000 INFO @ Thu, 09 Dec 2021 06:30:10: 4000000 INFO @ Thu, 09 Dec 2021 06:30:11: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 06:30:26: 10000000 INFO @ Thu, 09 Dec 2021 06:30:26: 7000000 INFO @ Thu, 09 Dec 2021 06:30:27: 5000000 INFO @ Thu, 09 Dec 2021 06:30:41: 11000000 INFO @ Thu, 09 Dec 2021 06:30:44: 8000000 INFO @ Thu, 09 Dec 2021 06:30:45: 6000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 06:30:57: 12000000 INFO @ Thu, 09 Dec 2021 06:31:00: 9000000 INFO @ Thu, 09 Dec 2021 06:31:03: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 06:31:03: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 06:31:03: #1 total tags in treatment: 3741520 INFO @ Thu, 09 Dec 2021 06:31:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 06:31:03: #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 06:31:03: #1 tags after filtering in treatment: 2036113 INFO @ Thu, 09 Dec 2021 06:31:03: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 09 Dec 2021 06:31:03: #1 finished! INFO @ Thu, 09 Dec 2021 06:31:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 06:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 06:31:03: #2 number of paired peaks: 1054 INFO @ Thu, 09 Dec 2021 06:31:03: start model_add_line... INFO @ Thu, 09 Dec 2021 06:31:03: start X-correlation... INFO @ Thu, 09 Dec 2021 06:31:03: end of X-cor INFO @ Thu, 09 Dec 2021 06:31:03: #2 finished! INFO @ Thu, 09 Dec 2021 06:31:03: #2 predicted fragment length is 298 bps INFO @ Thu, 09 Dec 2021 06:31:03: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 09 Dec 2021 06:31:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.05_model.r INFO @ Thu, 09 Dec 2021 06:31:03: 7000000 WARNING @ Thu, 09 Dec 2021 06:31:03: #2 Since the d (298) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 06:31:03: #2 You may need to consider one of the other alternative d(s): 298 WARNING @ Thu, 09 Dec 2021 06:31:03: #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 06:31:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 06:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 06:31:14: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 06:31:17: 10000000 INFO @ Thu, 09 Dec 2021 06:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.05_peaks.xls INFO @ Thu, 09 Dec 2021 06:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 06:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.05_summits.bed INFO @ Thu, 09 Dec 2021 06:31:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 06:31:21: 8000000 INFO @ Thu, 09 Dec 2021 06:31:33: 11000000 INFO @ Thu, 09 Dec 2021 06:31:37: 9000000 INFO @ Thu, 09 Dec 2021 06:31:49: 12000000 INFO @ Thu, 09 Dec 2021 06:31:52: 10000000 INFO @ Thu, 09 Dec 2021 06:31:55: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 06:31:55: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 06:31:55: #1 total tags in treatment: 3741520 INFO @ Thu, 09 Dec 2021 06:31:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 06:31:55: #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 06:31:55: #1 tags after filtering in treatment: 2036113 INFO @ Thu, 09 Dec 2021 06:31:55: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 09 Dec 2021 06:31:55: #1 finished! INFO @ Thu, 09 Dec 2021 06:31:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 06:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 06:31:55: #2 number of paired peaks: 1054 INFO @ Thu, 09 Dec 2021 06:31:55: start model_add_line... INFO @ Thu, 09 Dec 2021 06:31:55: start X-correlation... INFO @ Thu, 09 Dec 2021 06:31:55: end of X-cor INFO @ Thu, 09 Dec 2021 06:31:55: #2 finished! INFO @ Thu, 09 Dec 2021 06:31:55: #2 predicted fragment length is 298 bps INFO @ Thu, 09 Dec 2021 06:31:55: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 09 Dec 2021 06:31:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.10_model.r WARNING @ Thu, 09 Dec 2021 06:31:55: #2 Since the d (298) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 06:31:55: #2 You may need to consider one of the other alternative d(s): 298 WARNING @ Thu, 09 Dec 2021 06:31:55: #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 06:31:55: #3 Call peaks... INFO @ Thu, 09 Dec 2021 06:31:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 06:32:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 06:32:07: 11000000 INFO @ Thu, 09 Dec 2021 06:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.10_peaks.xls INFO @ Thu, 09 Dec 2021 06:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 06:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.10_summits.bed INFO @ Thu, 09 Dec 2021 06:32:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 06:32:21: 12000000 INFO @ Thu, 09 Dec 2021 06:32:26: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 06:32:26: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 06:32:26: #1 total tags in treatment: 3741520 INFO @ Thu, 09 Dec 2021 06:32:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 06:32:26: #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 06:32:26: #1 tags after filtering in treatment: 2036113 INFO @ Thu, 09 Dec 2021 06:32:26: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 09 Dec 2021 06:32:26: #1 finished! INFO @ Thu, 09 Dec 2021 06:32:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 06:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 06:32:27: #2 number of paired peaks: 1054 INFO @ Thu, 09 Dec 2021 06:32:27: start model_add_line... INFO @ Thu, 09 Dec 2021 06:32:27: start X-correlation... INFO @ Thu, 09 Dec 2021 06:32:27: end of X-cor INFO @ Thu, 09 Dec 2021 06:32:27: #2 finished! INFO @ Thu, 09 Dec 2021 06:32:27: #2 predicted fragment length is 298 bps INFO @ Thu, 09 Dec 2021 06:32:27: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 09 Dec 2021 06:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.20_model.r WARNING @ Thu, 09 Dec 2021 06:32:27: #2 Since the d (298) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 06:32:27: #2 You may need to consider one of the other alternative d(s): 298 WARNING @ Thu, 09 Dec 2021 06:32:27: #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 06:32:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 06:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 06:32:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 06:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.20_peaks.xls INFO @ Thu, 09 Dec 2021 06:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 06:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567170/SRX9567170.20_summits.bed INFO @ Thu, 09 Dec 2021 06:32:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis CompletedMACS2peakCalling