[2024-01-24 11:05:34,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference
[2024-01-24 11:05:35,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,718] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a79e0a8-0211-4c2f-88dd-8e90491dd9a1/GCF_003129565.1_ASM312956v1_genomic.fna.gz | prodigal -d GCF_003129565.1_ASM312956v1_genomic.fna/cds.fna -a GCF_003129565.1_ASM312956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:45,672] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:45,673] [INFO] Task started: HMMsearch
[2024-01-24 11:05:45,673] [INFO] Running command: hmmsearch --tblout GCF_003129565.1_ASM312956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference/reference_markers.hmm GCF_003129565.1_ASM312956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:45,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:45,955] [INFO] Found 6/6 markers.
[2024-01-24 11:05:45,987] [INFO] Query marker FASTA was written to GCF_003129565.1_ASM312956v1_genomic.fna/markers.fasta
[2024-01-24 11:05:45,988] [INFO] Task started: Blastn
[2024-01-24 11:05:45,988] [INFO] Running command: blastn -query GCF_003129565.1_ASM312956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference/reference_markers.fasta -out GCF_003129565.1_ASM312956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:46,861] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:46,866] [INFO] Selected 24 target genomes.
[2024-01-24 11:05:46,866] [INFO] Target genome list was writen to GCF_003129565.1_ASM312956v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:46,899] [INFO] Task started: fastANI
[2024-01-24 11:05:46,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a79e0a8-0211-4c2f-88dd-8e90491dd9a1/GCF_003129565.1_ASM312956v1_genomic.fna.gz --refList GCF_003129565.1_ASM312956v1_genomic.fna/target_genomes.txt --output GCF_003129565.1_ASM312956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:03,793] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:03,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:03,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:03,814] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:03,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:03,815] [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
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	100.0	1065	1066	95	conclusive
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	82.5758	689	1066	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.0314	461	1066	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.0249	452	1066	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.84	423	1066	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.8327	413	1066	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.7132	369	1066	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.6303	379	1066	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.5843	430	1066	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5818	400	1066	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.5476	401	1066	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.5259	420	1066	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.521	397	1066	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.4855	398	1066	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.452	403	1066	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.445	384	1066	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.4057	385	1066	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.2268	361	1066	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	78.2201	348	1066	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.1694	347	1066	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.1106	387	1066	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.0567	390	1066	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.9832	383	1066	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.6758	328	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:03,816] [INFO] DFAST Taxonomy check result was written to GCF_003129565.1_ASM312956v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:03,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:03,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:03,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference/checkm_data
[2024-01-24 11:06:03,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:03,856] [INFO] Task started: CheckM
[2024-01-24 11:06:03,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003129565.1_ASM312956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003129565.1_ASM312956v1_genomic.fna/checkm_input GCF_003129565.1_ASM312956v1_genomic.fna/checkm_result
[2024-01-24 11:06:37,768] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:37,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,797] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:37,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:37,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003129565.1_ASM312956v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:37,798] [INFO] Task started: Blastn
[2024-01-24 11:06:37,798] [INFO] Running command: blastn -query GCF_003129565.1_ASM312956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d08052d-740f-4d27-bb35-79f4ad2bfdb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003129565.1_ASM312956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:39,232] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:39,236] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:39,237] [INFO] Target genome list was writen to GCF_003129565.1_ASM312956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:39,251] [INFO] Task started: fastANI
[2024-01-24 11:06:39,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a79e0a8-0211-4c2f-88dd-8e90491dd9a1/GCF_003129565.1_ASM312956v1_genomic.fna.gz --refList GCF_003129565.1_ASM312956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003129565.1_ASM312956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:50,913] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:50,929] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:50,929] [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_003129565.1	s__Salibaculum griseiflavum	100.0	1065	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009908505.1	s__Salibaculum sp009908505	87.8265	783	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	82.5758	689	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	80.0317	606	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.3468	489	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004145845.1	s__Marivivens sp004145845	78.9325	518	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	78.4937	402	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	78.4816	403	1066	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_009789075.1	s__Pseudooceanicola pacificus	78.4812	274	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	78.3488	394	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.3468	446	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_001975705.1	s__Salipiger abyssi	78.3413	419	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	78.2659	378	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.1124	384	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_900116005.1	s__Poseidonocella sedimentorum	77.8555	316	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:50,930] [INFO] GTDB search result was written to GCF_003129565.1_ASM312956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:50,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:50,935] [INFO] DFAST_QC result json was written to GCF_003129565.1_ASM312956v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:50,935] [INFO] DFAST_QC completed!
[2024-01-24 11:06:50,935] [INFO] Total running time: 0h1m16s