[2024-01-24 12:31:58,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference
[2024-01-24 12:31:59,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,728] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a443448-53e2-4d37-a44e-4c89730d70ca/GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/cds.fna -a GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:17,398] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:17,399] [INFO] Task started: HMMsearch
[2024-01-24 12:32:17,399] [INFO] Running command: hmmsearch --tblout GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference/reference_markers.hmm GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:17,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:17,707] [INFO] Found 6/6 markers.
[2024-01-24 12:32:17,762] [INFO] Query marker FASTA was written to GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:32:17,762] [INFO] Task started: Blastn
[2024-01-24 12:32:17,762] [INFO] Running command: blastn -query GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference/reference_markers.fasta -out GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:18,700] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:18,704] [INFO] Selected 22 target genomes.
[2024-01-24 12:32:18,705] [INFO] Target genome list was writen to GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:32:18,711] [INFO] Task started: fastANI
[2024-01-24 12:32:18,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a443448-53e2-4d37-a44e-4c89730d70ca/GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna.gz --refList GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:37,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:37,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:37,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:37,564] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:37,564] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:37,564] [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
Aliiruegeria lutimaris	strain=DSM 25294	GCA_900099935.1	571298	571298	type	True	100.0	1837	1843	95	conclusive
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	91.2907	1400	1843	95	below_threshold
Aliiruegeria haliotis	strain=DSM 29328	GCA_003003255.1	1280846	1280846	type	True	79.7329	640	1843	95	below_threshold
Tropicimonas isoalkanivorans	strain=DSM 19548	GCA_900112335.1	441112	441112	type	True	78.7671	551	1843	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.0058	405	1843	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.9486	374	1843	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9141	379	1843	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.8471	376	1843	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.8419	460	1843	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.8255	383	1843	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.8153	404	1843	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.7987	401	1843	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.7124	290	1843	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6545	332	1843	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	77.4738	369	1843	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	77.4194	293	1843	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.4166	413	1843	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3866	306	1843	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	77.3581	303	1843	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.3375	348	1843	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.2831	347	1843	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.2129	221	1843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:37,567] [INFO] DFAST Taxonomy check result was written to GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:37,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:37,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:37,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference/checkm_data
[2024-01-24 12:32:37,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:37,628] [INFO] Task started: CheckM
[2024-01-24 12:32:37,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/checkm_input GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:33:28,306] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:28,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:28,331] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:28,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:28,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:33:28,333] [INFO] Task started: Blastn
[2024-01-24 12:33:28,333] [INFO] Running command: blastn -query GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg215f182b-ef84-4aad-b1d2-0baa7d0bb821/dqc_reference/reference_markers_gtdb.fasta -out GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:29,791] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:29,794] [INFO] Selected 12 target genomes.
[2024-01-24 12:33:29,795] [INFO] Target genome list was writen to GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:29,804] [INFO] Task started: fastANI
[2024-01-24 12:33:29,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a443448-53e2-4d37-a44e-4c89730d70ca/GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna.gz --refList GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:41,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:41,787] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:41,787] [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_900099935.1	s__Tropicimonas lutimaris	100.0	1837	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001558155.1	s__Tropicimonas sabulilitoris	91.2908	1400	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900188335.1	s__Tropicimonas sediminicola	80.7516	797	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004146235.1	s__Tropicimonas sp004146235	80.6287	873	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003255.1	s__Tropicimonas haliotis	79.7419	638	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112335.1	s__Tropicimonas isoalkanivorans	78.7849	550	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.6018	486	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.9945	388	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.9178	512	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	77.7417	413	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	77.6141	370	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	77.5859	315	1843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:41,789] [INFO] GTDB search result was written to GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:41,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:41,797] [INFO] DFAST_QC result json was written to GCF_900099935.1_IMG-taxon_2622736598_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:33:41,798] [INFO] DFAST_QC completed!
[2024-01-24 12:33:41,798] [INFO] Total running time: 0h1m44s