[2024-01-24 10:57:25,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:25,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:25,726] [INFO] DQC Reference Directory: /var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference
[2024-01-24 10:57:27,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,042] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg664a2535-66ba-4625-ba29-205eb551dcd1/GCF_002744735.1_ASM274473v1_genomic.fna.gz | prodigal -d GCF_002744735.1_ASM274473v1_genomic.fna/cds.fna -a GCF_002744735.1_ASM274473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:40,581] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:40,582] [INFO] Task started: HMMsearch
[2024-01-24 10:57:40,582] [INFO] Running command: hmmsearch --tblout GCF_002744735.1_ASM274473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference/reference_markers.hmm GCF_002744735.1_ASM274473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:40,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:40,919] [INFO] Found 6/6 markers.
[2024-01-24 10:57:40,956] [INFO] Query marker FASTA was written to GCF_002744735.1_ASM274473v1_genomic.fna/markers.fasta
[2024-01-24 10:57:40,957] [INFO] Task started: Blastn
[2024-01-24 10:57:40,957] [INFO] Running command: blastn -query GCF_002744735.1_ASM274473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference/reference_markers.fasta -out GCF_002744735.1_ASM274473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:41,698] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:41,701] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:41,701] [INFO] Target genome list was writen to GCF_002744735.1_ASM274473v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:41,734] [INFO] Task started: fastANI
[2024-01-24 10:57:41,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg664a2535-66ba-4625-ba29-205eb551dcd1/GCF_002744735.1_ASM274473v1_genomic.fna.gz --refList GCF_002744735.1_ASM274473v1_genomic.fna/target_genomes.txt --output GCF_002744735.1_ASM274473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:55,076] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:55,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:55,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:55,089] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:55,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:55,090] [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
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	100.0	1475	1476	95	conclusive
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	84.6595	1057	1476	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	83.3964	1004	1476	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	83.0748	949	1476	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	83.01	986	1476	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	82.648	941	1476	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	81.3589	818	1476	95	below_threshold
Marinobacter salinus	strain=Hb8	GCA_001854125.1	1874317	1874317	type	True	80.8861	732	1476	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	80.4604	715	1476	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	80.3211	630	1476	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.1825	582	1476	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	80.0927	665	1476	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	79.242	457	1476	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	79.033	500	1476	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.7731	432	1476	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:55,091] [INFO] DFAST Taxonomy check result was written to GCF_002744735.1_ASM274473v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:55,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:55,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:55,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference/checkm_data
[2024-01-24 10:57:55,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:55,135] [INFO] Task started: CheckM
[2024-01-24 10:57:55,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002744735.1_ASM274473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002744735.1_ASM274473v1_genomic.fna/checkm_input GCF_002744735.1_ASM274473v1_genomic.fna/checkm_result
[2024-01-24 10:58:36,707] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:36,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:36,731] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:36,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:36,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002744735.1_ASM274473v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:36,732] [INFO] Task started: Blastn
[2024-01-24 10:58:36,732] [INFO] Running command: blastn -query GCF_002744735.1_ASM274473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1aac8db-db13-4195-9550-cda62b2bf047/dqc_reference/reference_markers_gtdb.fasta -out GCF_002744735.1_ASM274473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:37,727] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:37,730] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:37,730] [INFO] Target genome list was writen to GCF_002744735.1_ASM274473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:37,740] [INFO] Task started: fastANI
[2024-01-24 10:58:37,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg664a2535-66ba-4625-ba29-205eb551dcd1/GCF_002744735.1_ASM274473v1_genomic.fna.gz --refList GCF_002744735.1_ASM274473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002744735.1_ASM274473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:50,680] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:50,693] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:50,693] [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_002744735.1	s__Marinobacter guineae	100.0	1475	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003441595.1	s__Marinobacter sp003441595	88.2835	1051	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707215.1	s__Marinobacter sp002707215	86.6108	542	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	84.6595	1057	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_002933275.1	s__Marinobacter maroccanus	83.4072	1002	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	83.0633	580	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	82.8787	934	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_008107725.1	s__Marinobacter sp008107725	82.8487	956	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	82.8013	954	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	82.648	941	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900115175.1	s__Marinobacter gudaonensis	81.3735	816	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860425.1	s__Marinobacter sp018860425	81.3647	797	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854125.1	s__Marinobacter salinus	80.9117	732	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:50,696] [INFO] GTDB search result was written to GCF_002744735.1_ASM274473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:50,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:50,702] [INFO] DFAST_QC result json was written to GCF_002744735.1_ASM274473v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:50,702] [INFO] DFAST_QC completed!
[2024-01-24 10:58:50,702] [INFO] Total running time: 0h1m25s