Job ID = 5720156 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,994,809 reads read : 43,989,618 reads written : 21,994,809 reads 0-length : 21,994,809 2020-04-15T12:26:24 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 39,096,930 reads read : 78,193,860 reads written : 39,096,930 reads 0-length : 39,096,930 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: 00:13:15 61091739 reads; of these: 61091739 (100.00%) were unpaired; of these: 28780008 (47.11%) aligned 0 times 25525331 (41.78%) aligned exactly 1 time 6786400 (11.11%) aligned >1 times 52.89% overall alignment rate Time searching: 00:13:15 Overall time: 00:13:16 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_rmdupse_core] 18419273 / 32311731 = 0.5700 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.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, 15 Apr 2020 22:00:22: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:00:22: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:00:28: 1000000 INFO @ Wed, 15 Apr 2020 22:00:34: 2000000 INFO @ Wed, 15 Apr 2020 22:00:40: 3000000 INFO @ Wed, 15 Apr 2020 22:00:46: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.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, 15 Apr 2020 22:00:51: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:00:51: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:00:53: 5000000 INFO @ Wed, 15 Apr 2020 22:00:57: 1000000 INFO @ Wed, 15 Apr 2020 22:00:59: 6000000 INFO @ Wed, 15 Apr 2020 22:01:04: 2000000 INFO @ Wed, 15 Apr 2020 22:01:05: 7000000 INFO @ Wed, 15 Apr 2020 22:01:10: 3000000 INFO @ Wed, 15 Apr 2020 22:01:11: 8000000 INFO @ Wed, 15 Apr 2020 22:01:16: 4000000 INFO @ Wed, 15 Apr 2020 22:01:17: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.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, 15 Apr 2020 22:01:21: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:01:21: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:01:23: 5000000 INFO @ Wed, 15 Apr 2020 22:01:24: 10000000 INFO @ Wed, 15 Apr 2020 22:01:28: 1000000 INFO @ Wed, 15 Apr 2020 22:01:30: 6000000 INFO @ Wed, 15 Apr 2020 22:01:30: 11000000 INFO @ Wed, 15 Apr 2020 22:01:35: 2000000 INFO @ Wed, 15 Apr 2020 22:01:36: 7000000 INFO @ Wed, 15 Apr 2020 22:01:37: 12000000 INFO @ Wed, 15 Apr 2020 22:01:42: 3000000 INFO @ Wed, 15 Apr 2020 22:01:43: 8000000 INFO @ Wed, 15 Apr 2020 22:01:44: 13000000 INFO @ Wed, 15 Apr 2020 22:01:49: 9000000 INFO @ Wed, 15 Apr 2020 22:01:49: 4000000 INFO @ Wed, 15 Apr 2020 22:01:51: #1 tag size is determined as 57 bps INFO @ Wed, 15 Apr 2020 22:01:51: #1 tag size = 57 INFO @ Wed, 15 Apr 2020 22:01:51: #1 total tags in treatment: 13892458 INFO @ Wed, 15 Apr 2020 22:01:51: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:01:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:01:51: #1 tags after filtering in treatment: 13892458 INFO @ Wed, 15 Apr 2020 22:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:01:51: #1 finished! INFO @ Wed, 15 Apr 2020 22:01:51: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:01:52: #2 number of paired peaks: 318 WARNING @ Wed, 15 Apr 2020 22:01:52: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 15 Apr 2020 22:01:52: start model_add_line... INFO @ Wed, 15 Apr 2020 22:01:52: start X-correlation... INFO @ Wed, 15 Apr 2020 22:01:52: end of X-cor INFO @ Wed, 15 Apr 2020 22:01:52: #2 finished! INFO @ Wed, 15 Apr 2020 22:01:52: #2 predicted fragment length is 2 bps INFO @ Wed, 15 Apr 2020 22:01:52: #2 alternative fragment length(s) may be 2,12,39,565 bps INFO @ Wed, 15 Apr 2020 22:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.05_model.r WARNING @ Wed, 15 Apr 2020 22:01:52: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:01:52: #2 You may need to consider one of the other alternative d(s): 2,12,39,565 WARNING @ Wed, 15 Apr 2020 22:01:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:01:52: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:01:55: 10000000 INFO @ Wed, 15 Apr 2020 22:01:55: 5000000 INFO @ Wed, 15 Apr 2020 22:02:02: 6000000 INFO @ Wed, 15 Apr 2020 22:02:02: 11000000 INFO @ Wed, 15 Apr 2020 22:02:08: 7000000 INFO @ Wed, 15 Apr 2020 22:02:08: 12000000 INFO @ Wed, 15 Apr 2020 22:02:14: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:02:14: 8000000 INFO @ Wed, 15 Apr 2020 22:02:15: 13000000 INFO @ Wed, 15 Apr 2020 22:02:20: 9000000 INFO @ Wed, 15 Apr 2020 22:02:20: #1 tag size is determined as 57 bps INFO @ Wed, 15 Apr 2020 22:02:20: #1 tag size = 57 INFO @ Wed, 15 Apr 2020 22:02:20: #1 total tags in treatment: 13892458 INFO @ Wed, 15 Apr 2020 22:02:20: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:02:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:02:21: #1 tags after filtering in treatment: 13892458 INFO @ Wed, 15 Apr 2020 22:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:02:21: #1 finished! INFO @ Wed, 15 Apr 2020 22:02:21: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:02:22: #2 number of paired peaks: 318 WARNING @ Wed, 15 Apr 2020 22:02:22: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 15 Apr 2020 22:02:22: start model_add_line... INFO @ Wed, 15 Apr 2020 22:02:22: start X-correlation... INFO @ Wed, 15 Apr 2020 22:02:22: end of X-cor INFO @ Wed, 15 Apr 2020 22:02:22: #2 finished! INFO @ Wed, 15 Apr 2020 22:02:22: #2 predicted fragment length is 2 bps INFO @ Wed, 15 Apr 2020 22:02:22: #2 alternative fragment length(s) may be 2,12,39,565 bps INFO @ Wed, 15 Apr 2020 22:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.10_model.r WARNING @ Wed, 15 Apr 2020 22:02:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:02:22: #2 You may need to consider one of the other alternative d(s): 2,12,39,565 WARNING @ Wed, 15 Apr 2020 22:02:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:02:22: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:02:26: 10000000 INFO @ Wed, 15 Apr 2020 22:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.05_summits.bed INFO @ Wed, 15 Apr 2020 22:02:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:02:32: 11000000 INFO @ Wed, 15 Apr 2020 22:02:39: 12000000 INFO @ Wed, 15 Apr 2020 22:02:43: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:02:45: 13000000 INFO @ Wed, 15 Apr 2020 22:02:50: #1 tag size is determined as 57 bps INFO @ Wed, 15 Apr 2020 22:02:50: #1 tag size = 57 INFO @ Wed, 15 Apr 2020 22:02:50: #1 total tags in treatment: 13892458 INFO @ Wed, 15 Apr 2020 22:02:50: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:02:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:02:50: #1 tags after filtering in treatment: 13892458 INFO @ Wed, 15 Apr 2020 22:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:02:50: #1 finished! INFO @ Wed, 15 Apr 2020 22:02:50: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:02:51: #2 number of paired peaks: 318 WARNING @ Wed, 15 Apr 2020 22:02:51: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 15 Apr 2020 22:02:51: start model_add_line... INFO @ Wed, 15 Apr 2020 22:02:51: start X-correlation... INFO @ Wed, 15 Apr 2020 22:02:51: end of X-cor INFO @ Wed, 15 Apr 2020 22:02:51: #2 finished! INFO @ Wed, 15 Apr 2020 22:02:51: #2 predicted fragment length is 2 bps INFO @ Wed, 15 Apr 2020 22:02:51: #2 alternative fragment length(s) may be 2,12,39,565 bps INFO @ Wed, 15 Apr 2020 22:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.20_model.r WARNING @ Wed, 15 Apr 2020 22:02:51: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:02:51: #2 You may need to consider one of the other alternative d(s): 2,12,39,565 WARNING @ Wed, 15 Apr 2020 22:02:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:02:51: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:02:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:02:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:02:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.10_summits.bed INFO @ Wed, 15 Apr 2020 22:02:56: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:03:13: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702598/SRX5702598.20_summits.bed INFO @ Wed, 15 Apr 2020 22:03:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。