[2024-01-24 12:27:18,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:18,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:18,925] [INFO] DQC Reference Directory: /var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference
[2024-01-24 12:27:20,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,079] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,080] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eb2281e-872c-4320-aed3-184f9e1e7b72/GCF_003008555.2_ASM300855v2_genomic.fna.gz | prodigal -d GCF_003008555.2_ASM300855v2_genomic.fna/cds.fna -a GCF_003008555.2_ASM300855v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:32,625] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:32,626] [INFO] Task started: HMMsearch
[2024-01-24 12:27:32,626] [INFO] Running command: hmmsearch --tblout GCF_003008555.2_ASM300855v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference/reference_markers.hmm GCF_003008555.2_ASM300855v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:32,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:32,830] [INFO] Found 6/6 markers.
[2024-01-24 12:27:32,866] [INFO] Query marker FASTA was written to GCF_003008555.2_ASM300855v2_genomic.fna/markers.fasta
[2024-01-24 12:27:32,866] [INFO] Task started: Blastn
[2024-01-24 12:27:32,866] [INFO] Running command: blastn -query GCF_003008555.2_ASM300855v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference/reference_markers.fasta -out GCF_003008555.2_ASM300855v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:33,775] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:33,778] [INFO] Selected 23 target genomes.
[2024-01-24 12:27:33,779] [INFO] Target genome list was writen to GCF_003008555.2_ASM300855v2_genomic.fna/target_genomes.txt
[2024-01-24 12:27:33,843] [INFO] Task started: fastANI
[2024-01-24 12:27:33,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eb2281e-872c-4320-aed3-184f9e1e7b72/GCF_003008555.2_ASM300855v2_genomic.fna.gz --refList GCF_003008555.2_ASM300855v2_genomic.fna/target_genomes.txt --output GCF_003008555.2_ASM300855v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:51,343] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:51,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:51,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:51,361] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:27:51,361] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:27:51,361] [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
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.7633	723	1418	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.742	696	1418	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.5311	715	1418	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.3806	623	1418	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	80.3123	705	1418	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	80.2791	622	1418	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	79.9914	615	1418	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.9018	626	1418	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.2282	485	1418	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	79.2015	392	1418	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	79.0179	521	1418	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.855	462	1418	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.685	502	1418	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.6607	463	1418	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.658	431	1418	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.5524	506	1418	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.5493	508	1418	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.4777	402	1418	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4577	389	1418	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.4166	488	1418	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.4072	488	1418	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.2019	406	1418	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.4508	366	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:51,363] [INFO] DFAST Taxonomy check result was written to GCF_003008555.2_ASM300855v2_genomic.fna/tc_result.tsv
[2024-01-24 12:27:51,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:51,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:51,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference/checkm_data
[2024-01-24 12:27:51,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:51,403] [INFO] Task started: CheckM
[2024-01-24 12:27:51,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003008555.2_ASM300855v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003008555.2_ASM300855v2_genomic.fna/checkm_input GCF_003008555.2_ASM300855v2_genomic.fna/checkm_result
[2024-01-24 12:28:37,980] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:37,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:38,004] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:38,004] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:38,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003008555.2_ASM300855v2_genomic.fna/markers.fasta)
[2024-01-24 12:28:38,005] [INFO] Task started: Blastn
[2024-01-24 12:28:38,005] [INFO] Running command: blastn -query GCF_003008555.2_ASM300855v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge6839f6e-37a8-4843-bd22-5315a974a26a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003008555.2_ASM300855v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:39,596] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:39,599] [INFO] Selected 19 target genomes.
[2024-01-24 12:28:39,600] [INFO] Target genome list was writen to GCF_003008555.2_ASM300855v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:39,670] [INFO] Task started: fastANI
[2024-01-24 12:28:39,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eb2281e-872c-4320-aed3-184f9e1e7b72/GCF_003008555.2_ASM300855v2_genomic.fna.gz --refList GCF_003008555.2_ASM300855v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003008555.2_ASM300855v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:55,840] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:55,855] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:55,855] [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_003008555.2	s__Pukyongiella litopenaei	100.0	1416	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.941	633	1418	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_900109035.1	s__Cribrihabitans marinus	80.7812	721	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.7299	656	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900108275.1	s__Jhaorihella thermophila	80.4569	651	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	80.3222	451	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	80.3164	704	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_001507595.1	s__Ruegeria marisrubri	80.2791	622	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.8973	627	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	79.7201	648	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	79.5683	693	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_005938225.1	s__Arenibacterium halophilum	79.5548	597	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_019104745.1	s__CAU-1522 sp019104745	79.4918	574	1418	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_001441615.1	s__Roseovarius atlanticus	79.0702	515	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	79.0356	542	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709405.1	s__Marinibacterium sp002709405	78.9321	574	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	78.871	513	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_001262635.1	s__Aestuariivita boseongensis	78.5643	504	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.4306	491	1418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:55,857] [INFO] GTDB search result was written to GCF_003008555.2_ASM300855v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:55,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:55,861] [INFO] DFAST_QC result json was written to GCF_003008555.2_ASM300855v2_genomic.fna/dqc_result.json
[2024-01-24 12:28:55,862] [INFO] DFAST_QC completed!
[2024-01-24 12:28:55,862] [INFO] Total running time: 0h1m37s