[2024-01-24 10:47:11,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg8caaaac5-15e2-454b-8ca9-76d45b2595ba/GCF_002210095.1_ASM221009v1_genomic.fna.gz | prodigal -d GCF_002210095.1_ASM221009v1_genomic.fna/cds.fna -a GCF_002210095.1_ASM221009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:36,844] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:36,845] [INFO] Task started: HMMsearch
[2024-01-24 10:47:36,845] [INFO] Running command: hmmsearch --tblout GCF_002210095.1_ASM221009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference/reference_markers.hmm GCF_002210095.1_ASM221009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:37,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:37,153] [INFO] Found 6/6 markers.
[2024-01-24 10:47:37,204] [INFO] Query marker FASTA was written to GCF_002210095.1_ASM221009v1_genomic.fna/markers.fasta
[2024-01-24 10:47:37,204] [INFO] Task started: Blastn
[2024-01-24 10:47:37,204] [INFO] Running command: blastn -query GCF_002210095.1_ASM221009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference/reference_markers.fasta -out GCF_002210095.1_ASM221009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:38,249] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:38,253] [INFO] Selected 28 target genomes.
[2024-01-24 10:47:38,254] [INFO] Target genome list was writen to GCF_002210095.1_ASM221009v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:38,807] [INFO] Task started: fastANI
[2024-01-24 10:47:38,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caaaac5-15e2-454b-8ca9-76d45b2595ba/GCF_002210095.1_ASM221009v1_genomic.fna.gz --refList GCF_002210095.1_ASM221009v1_genomic.fna/target_genomes.txt --output GCF_002210095.1_ASM221009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:02,787] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:02,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:02,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:02,810] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:02,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:02,811] [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
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.0693	765	2021	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.9962	743	2021	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.8402	743	2021	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.544	709	2021	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.5152	719	2021	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.5079	635	2021	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.4835	636	2021	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.4346	661	2021	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.4108	655	2021	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	79.2692	684	2021	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	79.2643	358	2021	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.2067	596	2021	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.2026	609	2021	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.1759	687	2021	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.1355	557	2021	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.1077	615	2021	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	79.1035	717	2021	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.097	712	2021	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	79.0451	650	2021	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.0425	645	2021	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.9763	610	2021	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.7428	588	2021	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5595	540	2021	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.4215	502	2021	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.1715	518	2021	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	78.0244	448	2021	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.9527	453	2021	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8635	322	2021	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:02,812] [INFO] DFAST Taxonomy check result was written to GCF_002210095.1_ASM221009v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:02,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:02,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:02,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference/checkm_data
[2024-01-24 10:48:02,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:02,875] [INFO] Task started: CheckM
[2024-01-24 10:48:02,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002210095.1_ASM221009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002210095.1_ASM221009v1_genomic.fna/checkm_input GCF_002210095.1_ASM221009v1_genomic.fna/checkm_result
[2024-01-24 10:49:03,552] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:03,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:03,589] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:03,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:03,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002210095.1_ASM221009v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:03,590] [INFO] Task started: Blastn
[2024-01-24 10:49:03,590] [INFO] Running command: blastn -query GCF_002210095.1_ASM221009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg614bec19-4a65-4b75-9395-29e99da0ff13/dqc_reference/reference_markers_gtdb.fasta -out GCF_002210095.1_ASM221009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:05,103] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:05,107] [INFO] Selected 17 target genomes.
[2024-01-24 10:49:05,108] [INFO] Target genome list was writen to GCF_002210095.1_ASM221009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:05,122] [INFO] Task started: fastANI
[2024-01-24 10:49:05,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caaaac5-15e2-454b-8ca9-76d45b2595ba/GCF_002210095.1_ASM221009v1_genomic.fna.gz --refList GCF_002210095.1_ASM221009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002210095.1_ASM221009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:22,862] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:22,879] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:22,879] [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_002210095.1	s__Marinibacterium profundimaris	100.0	2017	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003217735.2	s__Marinibacterium sp003217735	84.0637	1303	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCA_002709405.1	s__Marinibacterium sp002709405	83.3441	1111	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.6228	726	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	80.3278	758	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	80.218	720	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	80.072	764	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCA_003511785.1	s__UBA7951 sp003511785	79.951	450	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.8706	738	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.524	711	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002300555.1	s__Salipiger sp002300555	79.4709	532	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.3438	462	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765275.1	s__Chachezhania sp009765275	79.2422	688	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	79.2341	611	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	79.1046	716	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_001458395.1	s__Leisingera aquaemixtae	78.9871	608	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_003385555.1	s__Rhodosalinus sediminis	78.5691	526	2021	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:22,881] [INFO] GTDB search result was written to GCF_002210095.1_ASM221009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:22,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:22,887] [INFO] DFAST_QC result json was written to GCF_002210095.1_ASM221009v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:22,888] [INFO] DFAST_QC completed!
[2024-01-24 10:49:22,888] [INFO] Total running time: 0h2m11s