Job ID = 14159056 SRX = SRX10641174 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: 00:22:50 15700166 reads; of these: 15700166 (100.00%) were paired; of these: 7728395 (49.22%) aligned concordantly 0 times 6728184 (42.85%) aligned concordantly exactly 1 time 1243587 (7.92%) aligned concordantly >1 times ---- 7728395 pairs aligned concordantly 0 times; of these: 2105326 (27.24%) aligned discordantly 1 time ---- 5623069 pairs aligned 0 times concordantly or discordantly; of these: 11246138 mates make up the pairs; of these: 10337193 (91.92%) aligned 0 times 435385 (3.87%) aligned exactly 1 time 473560 (4.21%) aligned >1 times 67.08% overall alignment rate Time searching: 00:22:50 Overall time: 00:22:50 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 16 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] 1110432 / 10044393 = 0.1106 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 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.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 19:13:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:13:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:13:53: 1000000 INFO @ Wed, 08 Dec 2021 19:14:00: 2000000 INFO @ Wed, 08 Dec 2021 19:14:08: 3000000 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 19:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.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 19:14:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:14:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:14:17: 4000000 INFO @ Wed, 08 Dec 2021 19:14:25: 1000000 INFO @ Wed, 08 Dec 2021 19:14:27: 5000000 INFO @ Wed, 08 Dec 2021 19:14:37: 2000000 INFO @ Wed, 08 Dec 2021 19:14:38: 6000000 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 19:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.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 19:14:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:14:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:14:49: 7000000 INFO @ Wed, 08 Dec 2021 19:14:49: 3000000 INFO @ Wed, 08 Dec 2021 19:14:56: 1000000 INFO @ Wed, 08 Dec 2021 19:15:00: 8000000 INFO @ Wed, 08 Dec 2021 19:15:01: 4000000 INFO @ Wed, 08 Dec 2021 19:15:07: 2000000 INFO @ Wed, 08 Dec 2021 19:15:11: 9000000 INFO @ Wed, 08 Dec 2021 19:15:13: 5000000 INFO @ Wed, 08 Dec 2021 19:15:18: 3000000 INFO @ Wed, 08 Dec 2021 19:15:22: 10000000 INFO @ Wed, 08 Dec 2021 19:15:25: 6000000 INFO @ Wed, 08 Dec 2021 19:15:29: 4000000 INFO @ Wed, 08 Dec 2021 19:15:33: 11000000 INFO @ Wed, 08 Dec 2021 19:15:36: 7000000 INFO @ Wed, 08 Dec 2021 19:15:41: 5000000 INFO @ Wed, 08 Dec 2021 19:15:44: 12000000 INFO @ Wed, 08 Dec 2021 19:15:48: 8000000 INFO @ Wed, 08 Dec 2021 19:15:52: 6000000 INFO @ Wed, 08 Dec 2021 19:15:56: 13000000 INFO @ Wed, 08 Dec 2021 19:15:59: 9000000 INFO @ Wed, 08 Dec 2021 19:16:03: 7000000 INFO @ Wed, 08 Dec 2021 19:16:07: 14000000 INFO @ Wed, 08 Dec 2021 19:16:10: 10000000 INFO @ Wed, 08 Dec 2021 19:16:14: 8000000 INFO @ Wed, 08 Dec 2021 19:16:18: 15000000 INFO @ Wed, 08 Dec 2021 19:16:21: 11000000 INFO @ Wed, 08 Dec 2021 19:16:25: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:16:29: 16000000 INFO @ Wed, 08 Dec 2021 19:16:32: 12000000 INFO @ Wed, 08 Dec 2021 19:16:36: 10000000 INFO @ Wed, 08 Dec 2021 19:16:40: 17000000 INFO @ Wed, 08 Dec 2021 19:16:43: 13000000 INFO @ Wed, 08 Dec 2021 19:16:48: 11000000 INFO @ Wed, 08 Dec 2021 19:16:52: 18000000 INFO @ Wed, 08 Dec 2021 19:16:55: 14000000 INFO @ Wed, 08 Dec 2021 19:16:59: 12000000 INFO @ Wed, 08 Dec 2021 19:17:01: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:17:01: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:17:01: #1 total tags in treatment: 7040368 INFO @ Wed, 08 Dec 2021 19:17:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:17:01: #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 19:17:01: #1 tags after filtering in treatment: 6544871 INFO @ Wed, 08 Dec 2021 19:17:01: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:17:01: #1 finished! INFO @ Wed, 08 Dec 2021 19:17:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:17:02: #2 number of paired peaks: 506 WARNING @ Wed, 08 Dec 2021 19:17:02: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Wed, 08 Dec 2021 19:17:02: start model_add_line... INFO @ Wed, 08 Dec 2021 19:17:02: start X-correlation... INFO @ Wed, 08 Dec 2021 19:17:02: end of X-cor INFO @ Wed, 08 Dec 2021 19:17:02: #2 finished! INFO @ Wed, 08 Dec 2021 19:17:02: #2 predicted fragment length is 221 bps INFO @ Wed, 08 Dec 2021 19:17:02: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 08 Dec 2021 19:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.05_model.r WARNING @ Wed, 08 Dec 2021 19:17:02: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:17:02: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 08 Dec 2021 19:17:02: #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 19:17:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:17:06: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:17:09: 13000000 INFO @ Wed, 08 Dec 2021 19:17:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:17:17: 16000000 INFO @ Wed, 08 Dec 2021 19:17:20: 14000000 INFO @ Wed, 08 Dec 2021 19:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.05_summits.bed INFO @ Wed, 08 Dec 2021 19:17:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:17:28: 17000000 INFO @ Wed, 08 Dec 2021 19:17:31: 15000000 INFO @ Wed, 08 Dec 2021 19:17:39: 18000000 INFO @ Wed, 08 Dec 2021 19:17:41: 16000000 INFO @ Wed, 08 Dec 2021 19:17:48: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:17:48: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:17:48: #1 total tags in treatment: 7040368 INFO @ Wed, 08 Dec 2021 19:17:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:17:48: #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 19:17:48: #1 tags after filtering in treatment: 6544871 INFO @ Wed, 08 Dec 2021 19:17:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:17:48: #1 finished! INFO @ Wed, 08 Dec 2021 19:17:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:17:48: #2 number of paired peaks: 506 WARNING @ Wed, 08 Dec 2021 19:17:48: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Wed, 08 Dec 2021 19:17:48: start model_add_line... INFO @ Wed, 08 Dec 2021 19:17:49: start X-correlation... INFO @ Wed, 08 Dec 2021 19:17:49: end of X-cor INFO @ Wed, 08 Dec 2021 19:17:49: #2 finished! INFO @ Wed, 08 Dec 2021 19:17:49: #2 predicted fragment length is 221 bps INFO @ Wed, 08 Dec 2021 19:17:49: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 08 Dec 2021 19:17:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.10_model.r WARNING @ Wed, 08 Dec 2021 19:17:49: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:17:49: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 08 Dec 2021 19:17:49: #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 19:17:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:17:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:17:51: 17000000 INFO @ Wed, 08 Dec 2021 19:18:01: 18000000 INFO @ Wed, 08 Dec 2021 19:18:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:18:09: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:18:09: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:18:09: #1 total tags in treatment: 7040368 INFO @ Wed, 08 Dec 2021 19:18:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:18:09: #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 19:18:09: #1 tags after filtering in treatment: 6544871 INFO @ Wed, 08 Dec 2021 19:18:09: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:18:09: #1 finished! INFO @ Wed, 08 Dec 2021 19:18:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:18:09: #2 number of paired peaks: 506 WARNING @ Wed, 08 Dec 2021 19:18:09: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Wed, 08 Dec 2021 19:18:09: start model_add_line... INFO @ Wed, 08 Dec 2021 19:18:09: start X-correlation... INFO @ Wed, 08 Dec 2021 19:18:09: end of X-cor INFO @ Wed, 08 Dec 2021 19:18:09: #2 finished! INFO @ Wed, 08 Dec 2021 19:18:09: #2 predicted fragment length is 221 bps INFO @ Wed, 08 Dec 2021 19:18:09: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 08 Dec 2021 19:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.20_model.r WARNING @ Wed, 08 Dec 2021 19:18:09: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:18:09: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 08 Dec 2021 19:18:09: #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 19:18:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.10_summits.bed INFO @ Wed, 08 Dec 2021 19:18:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:18:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641174/SRX10641174.20_summits.bed INFO @ Wed, 08 Dec 2021 19:18:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 3 millis CompletedMACS2peakCalling