Job ID = 12264828 SRX = SRX7687151 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32752234 spots for SRR11034894/SRR11034894.sra Written 32752234 spots for SRR11034894/SRR11034894.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265497 ("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: 00:51:09 32752234 reads; of these: 32752234 (100.00%) were paired; of these: 7634249 (23.31%) aligned concordantly 0 times 20663436 (63.09%) aligned concordantly exactly 1 time 4454549 (13.60%) aligned concordantly >1 times ---- 7634249 pairs aligned concordantly 0 times; of these: 5047040 (66.11%) aligned discordantly 1 time ---- 2587209 pairs aligned 0 times concordantly or discordantly; of these: 5174418 mates make up the pairs; of these: 3049650 (58.94%) aligned 0 times 788336 (15.24%) aligned exactly 1 time 1336432 (25.83%) aligned >1 times 95.34% overall alignment rate Time searching: 00:51:09 Overall time: 00:51:09 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 28 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] 13275670 / 30130445 = 0.4406 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.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 @ Sat, 03 Apr 2021 07:06:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:06:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:04: 1000000 INFO @ Sat, 03 Apr 2021 07:07:14: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.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 @ Sat, 03 Apr 2021 07:07:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:24: 3000000 INFO @ Sat, 03 Apr 2021 07:07:33: 4000000 INFO @ Sat, 03 Apr 2021 07:07:36: 1000000 INFO @ Sat, 03 Apr 2021 07:07:43: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:50: 2000000 INFO @ Sat, 03 Apr 2021 07:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.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 @ Sat, 03 Apr 2021 07:07:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:53: 6000000 INFO @ Sat, 03 Apr 2021 07:08:03: 1000000 INFO @ Sat, 03 Apr 2021 07:08:04: 7000000 INFO @ Sat, 03 Apr 2021 07:08:05: 3000000 INFO @ Sat, 03 Apr 2021 07:08:13: 2000000 INFO @ Sat, 03 Apr 2021 07:08:14: 8000000 INFO @ Sat, 03 Apr 2021 07:08:21: 4000000 INFO @ Sat, 03 Apr 2021 07:08:23: 3000000 INFO @ Sat, 03 Apr 2021 07:08:24: 9000000 INFO @ Sat, 03 Apr 2021 07:08:34: 4000000 INFO @ Sat, 03 Apr 2021 07:08:34: 10000000 INFO @ Sat, 03 Apr 2021 07:08:36: 5000000 INFO @ Sat, 03 Apr 2021 07:08:44: 5000000 INFO @ Sat, 03 Apr 2021 07:08:46: 11000000 INFO @ Sat, 03 Apr 2021 07:08:51: 6000000 INFO @ Sat, 03 Apr 2021 07:08:55: 6000000 INFO @ Sat, 03 Apr 2021 07:08:56: 12000000 INFO @ Sat, 03 Apr 2021 07:09:05: 7000000 INFO @ Sat, 03 Apr 2021 07:09:06: 13000000 INFO @ Sat, 03 Apr 2021 07:09:06: 7000000 INFO @ Sat, 03 Apr 2021 07:09:15: 8000000 INFO @ Sat, 03 Apr 2021 07:09:16: 14000000 INFO @ Sat, 03 Apr 2021 07:09:21: 8000000 INFO @ Sat, 03 Apr 2021 07:09:23: 9000000 INFO @ Sat, 03 Apr 2021 07:09:26: 15000000 INFO @ Sat, 03 Apr 2021 07:09:33: 10000000 INFO @ Sat, 03 Apr 2021 07:09:35: 9000000 INFO @ Sat, 03 Apr 2021 07:09:37: 16000000 INFO @ Sat, 03 Apr 2021 07:09:42: 11000000 INFO @ Sat, 03 Apr 2021 07:09:49: 17000000 INFO @ Sat, 03 Apr 2021 07:09:49: 10000000 INFO @ Sat, 03 Apr 2021 07:09:53: 12000000 INFO @ Sat, 03 Apr 2021 07:10:00: 18000000 INFO @ Sat, 03 Apr 2021 07:10:03: 13000000 INFO @ Sat, 03 Apr 2021 07:10:04: 11000000 INFO @ Sat, 03 Apr 2021 07:10:12: 19000000 INFO @ Sat, 03 Apr 2021 07:10:13: 14000000 INFO @ Sat, 03 Apr 2021 07:10:18: 12000000 INFO @ Sat, 03 Apr 2021 07:10:22: 20000000 INFO @ Sat, 03 Apr 2021 07:10:23: 15000000 INFO @ Sat, 03 Apr 2021 07:10:32: 13000000 INFO @ Sat, 03 Apr 2021 07:10:33: 21000000 INFO @ Sat, 03 Apr 2021 07:10:33: 16000000 INFO @ Sat, 03 Apr 2021 07:10:43: 22000000 INFO @ Sat, 03 Apr 2021 07:10:43: 17000000 INFO @ Sat, 03 Apr 2021 07:10:46: 14000000 INFO @ Sat, 03 Apr 2021 07:10:53: 23000000 INFO @ Sat, 03 Apr 2021 07:10:54: 18000000 INFO @ Sat, 03 Apr 2021 07:10:59: 15000000 INFO @ Sat, 03 Apr 2021 07:11:04: 24000000 INFO @ Sat, 03 Apr 2021 07:11:04: 19000000 INFO @ Sat, 03 Apr 2021 07:11:13: 16000000 INFO @ Sat, 03 Apr 2021 07:11:14: 20000000 INFO @ Sat, 03 Apr 2021 07:11:14: 25000000 INFO @ Sat, 03 Apr 2021 07:11:24: 21000000 INFO @ Sat, 03 Apr 2021 07:11:25: 26000000 INFO @ Sat, 03 Apr 2021 07:11:28: 17000000 INFO @ Sat, 03 Apr 2021 07:11:34: 27000000 INFO @ Sat, 03 Apr 2021 07:11:35: 22000000 INFO @ Sat, 03 Apr 2021 07:11:42: 18000000 INFO @ Sat, 03 Apr 2021 07:11:44: 28000000 INFO @ Sat, 03 Apr 2021 07:11:45: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:11:55: 29000000 INFO @ Sat, 03 Apr 2021 07:11:55: 24000000 INFO @ Sat, 03 Apr 2021 07:11:56: 19000000 INFO @ Sat, 03 Apr 2021 07:12:06: 30000000 INFO @ Sat, 03 Apr 2021 07:12:06: 25000000 INFO @ Sat, 03 Apr 2021 07:12:10: 20000000 INFO @ Sat, 03 Apr 2021 07:12:17: 31000000 INFO @ Sat, 03 Apr 2021 07:12:17: 26000000 INFO @ Sat, 03 Apr 2021 07:12:25: 21000000 INFO @ Sat, 03 Apr 2021 07:12:27: 27000000 INFO @ Sat, 03 Apr 2021 07:12:27: 32000000 INFO @ Sat, 03 Apr 2021 07:12:37: 33000000 INFO @ Sat, 03 Apr 2021 07:12:37: 28000000 INFO @ Sat, 03 Apr 2021 07:12:40: 22000000 INFO @ Sat, 03 Apr 2021 07:12:46: 34000000 INFO @ Sat, 03 Apr 2021 07:12:48: 29000000 INFO @ Sat, 03 Apr 2021 07:12:55: 23000000 INFO @ Sat, 03 Apr 2021 07:12:56: 35000000 INFO @ Sat, 03 Apr 2021 07:12:58: 30000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:13:05: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:13:05: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:13:05: #1 total tags in treatment: 13730491 INFO @ Sat, 03 Apr 2021 07:13:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:13:06: #1 tags after filtering in treatment: 10100807 INFO @ Sat, 03 Apr 2021 07:13:06: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:13:06: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:07: #2 number of paired peaks: 366 WARNING @ Sat, 03 Apr 2021 07:13:07: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:07: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:07: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:07: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:07: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:07: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 07:13:07: #2 alternative fragment length(s) may be 4,123,127,134 bps INFO @ Sat, 03 Apr 2021 07:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.05_model.r WARNING @ Sat, 03 Apr 2021 07:13:07: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:07: #2 You may need to consider one of the other alternative d(s): 4,123,127,134 WARNING @ Sat, 03 Apr 2021 07:13:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:13:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:13:08: 31000000 INFO @ Sat, 03 Apr 2021 07:13:09: 24000000 INFO @ Sat, 03 Apr 2021 07:13:20: 32000000 INFO @ Sat, 03 Apr 2021 07:13:23: 25000000 INFO @ Sat, 03 Apr 2021 07:13:32: 33000000 INFO @ Sat, 03 Apr 2021 07:13:39: 26000000 INFO @ Sat, 03 Apr 2021 07:13:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:45: 34000000 INFO @ Sat, 03 Apr 2021 07:13:54: 27000000 INFO @ Sat, 03 Apr 2021 07:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.05_summits.bed INFO @ Sat, 03 Apr 2021 07:13:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (499 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:13:58: 35000000 INFO @ Sat, 03 Apr 2021 07:14:09: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:14:09: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:14:09: #1 total tags in treatment: 13730491 INFO @ Sat, 03 Apr 2021 07:14:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:14:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:14:09: #1 tags after filtering in treatment: 10100807 INFO @ Sat, 03 Apr 2021 07:14:09: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:14:09: #1 finished! INFO @ Sat, 03 Apr 2021 07:14:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:14:10: #2 number of paired peaks: 366 WARNING @ Sat, 03 Apr 2021 07:14:10: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Sat, 03 Apr 2021 07:14:10: start model_add_line... INFO @ Sat, 03 Apr 2021 07:14:10: start X-correlation... INFO @ Sat, 03 Apr 2021 07:14:10: end of X-cor INFO @ Sat, 03 Apr 2021 07:14:10: #2 finished! INFO @ Sat, 03 Apr 2021 07:14:10: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 07:14:10: #2 alternative fragment length(s) may be 4,123,127,134 bps INFO @ Sat, 03 Apr 2021 07:14:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.20_model.r WARNING @ Sat, 03 Apr 2021 07:14:10: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:14:10: #2 You may need to consider one of the other alternative d(s): 4,123,127,134 WARNING @ Sat, 03 Apr 2021 07:14:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:14:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:14:10: 28000000 INFO @ Sat, 03 Apr 2021 07:14:25: 29000000 INFO @ Sat, 03 Apr 2021 07:14:38: 30000000 INFO @ Sat, 03 Apr 2021 07:14:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:14:51: 31000000 INFO @ Sat, 03 Apr 2021 07:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.20_summits.bed INFO @ Sat, 03 Apr 2021 07:14:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (158 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:15:05: 32000000 INFO @ Sat, 03 Apr 2021 07:15:18: 33000000 INFO @ Sat, 03 Apr 2021 07:15:31: 34000000 INFO @ Sat, 03 Apr 2021 07:15:44: 35000000 INFO @ Sat, 03 Apr 2021 07:15:55: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:15:55: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:15:55: #1 total tags in treatment: 13730491 INFO @ Sat, 03 Apr 2021 07:15:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:15:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:15:55: #1 tags after filtering in treatment: 10100807 INFO @ Sat, 03 Apr 2021 07:15:55: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:15:55: #1 finished! INFO @ Sat, 03 Apr 2021 07:15:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:15:56: #2 number of paired peaks: 366 WARNING @ Sat, 03 Apr 2021 07:15:56: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Sat, 03 Apr 2021 07:15:56: start model_add_line... INFO @ Sat, 03 Apr 2021 07:15:56: start X-correlation... INFO @ Sat, 03 Apr 2021 07:15:56: end of X-cor INFO @ Sat, 03 Apr 2021 07:15:56: #2 finished! INFO @ Sat, 03 Apr 2021 07:15:56: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 07:15:56: #2 alternative fragment length(s) may be 4,123,127,134 bps INFO @ Sat, 03 Apr 2021 07:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.10_model.r WARNING @ Sat, 03 Apr 2021 07:15:56: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:15:56: #2 You may need to consider one of the other alternative d(s): 4,123,127,134 WARNING @ Sat, 03 Apr 2021 07:15:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:15:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:16:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687151/SRX7687151.10_summits.bed INFO @ Sat, 03 Apr 2021 07:16:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 4 millis CompletedMACS2peakCalling