[2024-01-24 14:47:55,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference
[2024-01-24 14:47:58,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,522] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg5308d004-bdbc-4de8-ac3f-80a456f2d0de/GCF_900455185.1_56931_A02_genomic.fna.gz | prodigal -d GCF_900455185.1_56931_A02_genomic.fna/cds.fna -a GCF_900455185.1_56931_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:07,481] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:07,482] [INFO] Task started: HMMsearch
[2024-01-24 14:48:07,482] [INFO] Running command: hmmsearch --tblout GCF_900455185.1_56931_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference/reference_markers.hmm GCF_900455185.1_56931_A02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:07,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:07,829] [INFO] Found 6/6 markers.
[2024-01-24 14:48:07,878] [INFO] Query marker FASTA was written to GCF_900455185.1_56931_A02_genomic.fna/markers.fasta
[2024-01-24 14:48:07,878] [INFO] Task started: Blastn
[2024-01-24 14:48:07,878] [INFO] Running command: blastn -query GCF_900455185.1_56931_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference/reference_markers.fasta -out GCF_900455185.1_56931_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:08,639] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:08,643] [INFO] Selected 12 target genomes.
[2024-01-24 14:48:08,643] [INFO] Target genome list was writen to GCF_900455185.1_56931_A02_genomic.fna/target_genomes.txt
[2024-01-24 14:48:08,664] [INFO] Task started: fastANI
[2024-01-24 14:48:08,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg5308d004-bdbc-4de8-ac3f-80a456f2d0de/GCF_900455185.1_56931_A02_genomic.fna.gz --refList GCF_900455185.1_56931_A02_genomic.fna/target_genomes.txt --output GCF_900455185.1_56931_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:21,284] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:21,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:21,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:21,298] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:48:21,298] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:48:21,298] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	100.0	1421	1424	95	inconclusive
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	99.9725	1417	1424	95	inconclusive
Pseudoalteromonas nigrifaciens	strain=NBRC 103036	GCA_007991255.1	28109	28109	type	True	99.9082	1298	1424	95	inconclusive
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	96.0498	1190	1424	95	inconclusive
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	83.6254	906	1424	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	82.8723	853	1424	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	82.7911	833	1424	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	82.205	806	1424	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.5158	633	1424	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	77.0546	63	1424	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	76.3807	60	1424	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	76.1838	54	1424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:21,300] [INFO] DFAST Taxonomy check result was written to GCF_900455185.1_56931_A02_genomic.fna/tc_result.tsv
[2024-01-24 14:48:21,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:21,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:21,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference/checkm_data
[2024-01-24 14:48:21,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:21,346] [INFO] Task started: CheckM
[2024-01-24 14:48:21,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900455185.1_56931_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900455185.1_56931_A02_genomic.fna/checkm_input GCF_900455185.1_56931_A02_genomic.fna/checkm_result
[2024-01-24 14:48:52,259] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:52,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:52,285] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:52,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:52,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900455185.1_56931_A02_genomic.fna/markers.fasta)
[2024-01-24 14:48:52,287] [INFO] Task started: Blastn
[2024-01-24 14:48:52,287] [INFO] Running command: blastn -query GCF_900455185.1_56931_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg91eff3ea-3b59-453f-a7ba-26c59b5b55f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900455185.1_56931_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:53,422] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:53,426] [INFO] Selected 10 target genomes.
[2024-01-24 14:48:53,427] [INFO] Target genome list was writen to GCF_900455185.1_56931_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:53,436] [INFO] Task started: fastANI
[2024-01-24 14:48:53,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg5308d004-bdbc-4de8-ac3f-80a456f2d0de/GCF_900455185.1_56931_A02_genomic.fna.gz --refList GCF_900455185.1_56931_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900455185.1_56931_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:06,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:06,093] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:49:06,094] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002221505.1	s__Pseudoalteromonas nigrifaciens	99.9725	1417	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	inconclusive
GCF_001465295.1	s__Pseudoalteromonas translucida	96.0735	1191	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000238395.3	s__Pseudoalteromonas arctica	83.5969	908	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	82.8563	864	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCA_000814675.1	s__Pseudoalteromonas distincta	82.8533	857	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	82.7535	838	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	82.7183	868	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	82.6305	863	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	82.5139	819	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	79.9826	574	1424	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:06,095] [INFO] GTDB search result was written to GCF_900455185.1_56931_A02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:06,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:06,100] [INFO] DFAST_QC result json was written to GCF_900455185.1_56931_A02_genomic.fna/dqc_result.json
[2024-01-24 14:49:06,100] [INFO] DFAST_QC completed!
[2024-01-24 14:49:06,101] [INFO] Total running time: 0h1m10s