Job ID = 12264748 SRX = SRX2333001 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21992224 spots for SRR5000681/SRR5000681.sra Written 21992224 spots for SRR5000681/SRR5000681.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265438 ("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: 00:41:11 21992224 reads; of these: 21992224 (100.00%) were paired; of these: 7535600 (34.26%) aligned concordantly 0 times 11863739 (53.95%) aligned concordantly exactly 1 time 2592885 (11.79%) aligned concordantly >1 times ---- 7535600 pairs aligned concordantly 0 times; of these: 3510640 (46.59%) aligned discordantly 1 time ---- 4024960 pairs aligned 0 times concordantly or discordantly; of these: 8049920 mates make up the pairs; of these: 6490682 (80.63%) aligned 0 times 636469 (7.91%) aligned exactly 1 time 922769 (11.46%) aligned >1 times 85.24% overall alignment rate Time searching: 00:41:11 Overall time: 00:41:11 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] 1778252 / 17866760 = 0.0995 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 06:58:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.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 06:58:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:40: 1000000 INFO @ Sat, 03 Apr 2021 06:58:47: 2000000 INFO @ Sat, 03 Apr 2021 06:58:55: 3000000 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 06:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.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 06:59:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:02: 4000000 INFO @ Sat, 03 Apr 2021 06:59:10: 1000000 INFO @ Sat, 03 Apr 2021 06:59:10: 5000000 INFO @ Sat, 03 Apr 2021 06:59:17: 6000000 INFO @ Sat, 03 Apr 2021 06:59:18: 2000000 INFO @ Sat, 03 Apr 2021 06:59:25: 7000000 INFO @ Sat, 03 Apr 2021 06:59:26: 3000000 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 06:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.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 06:59:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:32: 8000000 INFO @ Sat, 03 Apr 2021 06:59:35: 4000000 INFO @ Sat, 03 Apr 2021 06:59:40: 9000000 INFO @ Sat, 03 Apr 2021 06:59:40: 1000000 INFO @ Sat, 03 Apr 2021 06:59:45: 5000000 INFO @ Sat, 03 Apr 2021 06:59:47: 10000000 INFO @ Sat, 03 Apr 2021 06:59:49: 2000000 INFO @ Sat, 03 Apr 2021 06:59:55: 11000000 INFO @ Sat, 03 Apr 2021 06:59:55: 6000000 INFO @ Sat, 03 Apr 2021 06:59:59: 3000000 INFO @ Sat, 03 Apr 2021 07:00:03: 12000000 INFO @ Sat, 03 Apr 2021 07:00:05: 7000000 INFO @ Sat, 03 Apr 2021 07:00:09: 4000000 INFO @ Sat, 03 Apr 2021 07:00:11: 13000000 INFO @ Sat, 03 Apr 2021 07:00:15: 8000000 INFO @ Sat, 03 Apr 2021 07:00:19: 14000000 INFO @ Sat, 03 Apr 2021 07:00:19: 5000000 INFO @ Sat, 03 Apr 2021 07:00:26: 9000000 INFO @ Sat, 03 Apr 2021 07:00:26: 15000000 INFO @ Sat, 03 Apr 2021 07:00:30: 6000000 INFO @ Sat, 03 Apr 2021 07:00:34: 16000000 INFO @ Sat, 03 Apr 2021 07:00:36: 10000000 INFO @ Sat, 03 Apr 2021 07:00:40: 7000000 INFO @ Sat, 03 Apr 2021 07:00:41: 17000000 INFO @ Sat, 03 Apr 2021 07:00:47: 11000000 INFO @ Sat, 03 Apr 2021 07:00:50: 18000000 INFO @ Sat, 03 Apr 2021 07:00:52: 8000000 INFO @ Sat, 03 Apr 2021 07:00:57: 12000000 INFO @ Sat, 03 Apr 2021 07:01:00: 19000000 INFO @ Sat, 03 Apr 2021 07:01:03: 9000000 INFO @ Sat, 03 Apr 2021 07:01:07: 13000000 INFO @ Sat, 03 Apr 2021 07:01:09: 20000000 INFO @ Sat, 03 Apr 2021 07:01:13: 10000000 INFO @ Sat, 03 Apr 2021 07:01:18: 14000000 INFO @ Sat, 03 Apr 2021 07:01:19: 21000000 INFO @ Sat, 03 Apr 2021 07:01:24: 11000000 INFO @ Sat, 03 Apr 2021 07:01:28: 22000000 INFO @ Sat, 03 Apr 2021 07:01:28: 15000000 INFO @ Sat, 03 Apr 2021 07:01:34: 12000000 INFO @ Sat, 03 Apr 2021 07:01:36: 23000000 INFO @ Sat, 03 Apr 2021 07:01:39: 16000000 INFO @ Sat, 03 Apr 2021 07:01:45: 13000000 INFO @ Sat, 03 Apr 2021 07:01:45: 24000000 INFO @ Sat, 03 Apr 2021 07:01:50: 17000000 INFO @ Sat, 03 Apr 2021 07:01:53: 25000000 INFO @ Sat, 03 Apr 2021 07:01:55: 14000000 INFO @ Sat, 03 Apr 2021 07:02:00: 18000000 INFO @ Sat, 03 Apr 2021 07:02:02: 26000000 INFO @ Sat, 03 Apr 2021 07:02:06: 15000000 INFO @ Sat, 03 Apr 2021 07:02:10: 19000000 INFO @ Sat, 03 Apr 2021 07:02:11: 27000000 INFO @ Sat, 03 Apr 2021 07:02:16: 16000000 INFO @ Sat, 03 Apr 2021 07:02:19: 28000000 INFO @ Sat, 03 Apr 2021 07:02:21: 20000000 INFO @ Sat, 03 Apr 2021 07:02:27: 17000000 INFO @ Sat, 03 Apr 2021 07:02:28: 29000000 INFO @ Sat, 03 Apr 2021 07:02:31: 21000000 INFO @ Sat, 03 Apr 2021 07:02:37: 18000000 INFO @ Sat, 03 Apr 2021 07:02:37: 30000000 INFO @ Sat, 03 Apr 2021 07:02:42: 22000000 INFO @ Sat, 03 Apr 2021 07:02:46: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:02:48: 19000000 INFO @ Sat, 03 Apr 2021 07:02:52: 23000000 INFO @ Sat, 03 Apr 2021 07:02:55: 32000000 INFO @ Sat, 03 Apr 2021 07:02:58: 20000000 INFO @ Sat, 03 Apr 2021 07:03:03: 24000000 INFO @ Sat, 03 Apr 2021 07:03:03: 33000000 INFO @ Sat, 03 Apr 2021 07:03:09: 21000000 INFO @ Sat, 03 Apr 2021 07:03:11: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:03:11: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:03:11: #1 total tags in treatment: 12910044 INFO @ Sat, 03 Apr 2021 07:03:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:03:11: #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 07:03:11: #1 tags after filtering in treatment: 9320315 INFO @ Sat, 03 Apr 2021 07:03:11: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 07:03:11: #1 finished! INFO @ Sat, 03 Apr 2021 07:03:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:03:12: #2 number of paired peaks: 211 WARNING @ Sat, 03 Apr 2021 07:03:12: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 03 Apr 2021 07:03:12: start model_add_line... INFO @ Sat, 03 Apr 2021 07:03:12: start X-correlation... INFO @ Sat, 03 Apr 2021 07:03:12: end of X-cor INFO @ Sat, 03 Apr 2021 07:03:12: #2 finished! INFO @ Sat, 03 Apr 2021 07:03:12: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 07:03:12: #2 alternative fragment length(s) may be 4,130,147,161 bps INFO @ Sat, 03 Apr 2021 07:03:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.05_model.r WARNING @ Sat, 03 Apr 2021 07:03:12: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:03:12: #2 You may need to consider one of the other alternative d(s): 4,130,147,161 WARNING @ Sat, 03 Apr 2021 07:03:12: #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 07:03:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:03:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:03:13: 25000000 INFO @ Sat, 03 Apr 2021 07:03:19: 22000000 INFO @ Sat, 03 Apr 2021 07:03:24: 26000000 INFO @ Sat, 03 Apr 2021 07:03:30: 23000000 INFO @ Sat, 03 Apr 2021 07:03:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:03:34: 27000000 INFO @ Sat, 03 Apr 2021 07:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.05_summits.bed INFO @ Sat, 03 Apr 2021 07:03:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:03:40: 24000000 INFO @ Sat, 03 Apr 2021 07:03:45: 28000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:03:51: 25000000 INFO @ Sat, 03 Apr 2021 07:03:55: 29000000 INFO @ Sat, 03 Apr 2021 07:04:01: 26000000 INFO @ Sat, 03 Apr 2021 07:04:06: 30000000 INFO @ Sat, 03 Apr 2021 07:04:12: 27000000 INFO @ Sat, 03 Apr 2021 07:04:16: 31000000 INFO @ Sat, 03 Apr 2021 07:04:22: 28000000 INFO @ Sat, 03 Apr 2021 07:04:26: 32000000 INFO @ Sat, 03 Apr 2021 07:04:32: 29000000 INFO @ Sat, 03 Apr 2021 07:04:36: 33000000 INFO @ Sat, 03 Apr 2021 07:04:42: 30000000 INFO @ Sat, 03 Apr 2021 07:04:46: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:04:46: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:04:46: #1 total tags in treatment: 12910044 INFO @ Sat, 03 Apr 2021 07:04:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:04:46: #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 07:04:46: #1 tags after filtering in treatment: 9320315 INFO @ Sat, 03 Apr 2021 07:04:46: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 07:04:46: #1 finished! INFO @ Sat, 03 Apr 2021 07:04:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:04:46: #2 number of paired peaks: 211 WARNING @ Sat, 03 Apr 2021 07:04:46: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 03 Apr 2021 07:04:46: start model_add_line... INFO @ Sat, 03 Apr 2021 07:04:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:04:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:04:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:04:47: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 07:04:47: #2 alternative fragment length(s) may be 4,130,147,161 bps INFO @ Sat, 03 Apr 2021 07:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.10_model.r WARNING @ Sat, 03 Apr 2021 07:04:47: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:04:47: #2 You may need to consider one of the other alternative d(s): 4,130,147,161 WARNING @ Sat, 03 Apr 2021 07:04:47: #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 07:04:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:04:51: 31000000 INFO @ Sat, 03 Apr 2021 07:05:00: 32000000 INFO @ Sat, 03 Apr 2021 07:05:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:05:08: 33000000 INFO @ Sat, 03 Apr 2021 07:05:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:05:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:05:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.10_summits.bed INFO @ Sat, 03 Apr 2021 07:05:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (224 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:05:16: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:05:16: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:05:16: #1 total tags in treatment: 12910044 INFO @ Sat, 03 Apr 2021 07:05:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:05:16: #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 07:05:17: #1 tags after filtering in treatment: 9320315 INFO @ Sat, 03 Apr 2021 07:05:17: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 07:05:17: #1 finished! INFO @ Sat, 03 Apr 2021 07:05:17: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:05:17: #2 number of paired peaks: 211 WARNING @ Sat, 03 Apr 2021 07:05:17: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sat, 03 Apr 2021 07:05:17: start model_add_line... INFO @ Sat, 03 Apr 2021 07:05:17: start X-correlation... INFO @ Sat, 03 Apr 2021 07:05:18: end of X-cor INFO @ Sat, 03 Apr 2021 07:05:18: #2 finished! INFO @ Sat, 03 Apr 2021 07:05:18: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 07:05:18: #2 alternative fragment length(s) may be 4,130,147,161 bps INFO @ Sat, 03 Apr 2021 07:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.20_model.r WARNING @ Sat, 03 Apr 2021 07:05:18: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:05:18: #2 You may need to consider one of the other alternative d(s): 4,130,147,161 WARNING @ Sat, 03 Apr 2021 07:05:18: #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 07:05:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:05:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:05:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:05:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:05:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333001/SRX2333001.20_summits.bed INFO @ Sat, 03 Apr 2021 07:05:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 1 millis CompletedMACS2peakCalling