[2024-01-24 10:47:22,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:22,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:22,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference
[2024-01-24 10:47:26,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,184] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg41f78205-03de-47eb-ba45-27fe262ec423/GCF_002087335.1_ASM208733v1_genomic.fna.gz | prodigal -d GCF_002087335.1_ASM208733v1_genomic.fna/cds.fna -a GCF_002087335.1_ASM208733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:40,715] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:40,715] [INFO] Task started: HMMsearch
[2024-01-24 10:47:40,715] [INFO] Running command: hmmsearch --tblout GCF_002087335.1_ASM208733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference/reference_markers.hmm GCF_002087335.1_ASM208733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:41,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:41,027] [INFO] Found 6/6 markers.
[2024-01-24 10:47:41,071] [INFO] Query marker FASTA was written to GCF_002087335.1_ASM208733v1_genomic.fna/markers.fasta
[2024-01-24 10:47:41,072] [INFO] Task started: Blastn
[2024-01-24 10:47:41,072] [INFO] Running command: blastn -query GCF_002087335.1_ASM208733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference/reference_markers.fasta -out GCF_002087335.1_ASM208733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:41,883] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:41,887] [INFO] Selected 20 target genomes.
[2024-01-24 10:47:41,887] [INFO] Target genome list was writen to GCF_002087335.1_ASM208733v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:41,896] [INFO] Task started: fastANI
[2024-01-24 10:47:41,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f78205-03de-47eb-ba45-27fe262ec423/GCF_002087335.1_ASM208733v1_genomic.fna.gz --refList GCF_002087335.1_ASM208733v1_genomic.fna/target_genomes.txt --output GCF_002087335.1_ASM208733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:59,177] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:59,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:59,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:59,193] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:59,193] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:59,193] [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
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	100.0	1527	1540	95	conclusive
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	82.2347	940	1540	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	81.7186	868	1540	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.6259	599	1540	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.4978	631	1540	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.4755	635	1540	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	78.4092	529	1540	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.3866	538	1540	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.3107	500	1540	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	78.2723	473	1540	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.2506	507	1540	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	77.987	379	1540	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.9761	396	1540	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	77.9059	384	1540	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.8772	393	1540	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.6181	307	1540	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.1823	307	1540	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.0811	272	1540	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.9823	263	1540	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.328	129	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:59,195] [INFO] DFAST Taxonomy check result was written to GCF_002087335.1_ASM208733v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:59,195] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:59,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:59,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference/checkm_data
[2024-01-24 10:47:59,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:59,241] [INFO] Task started: CheckM
[2024-01-24 10:47:59,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002087335.1_ASM208733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002087335.1_ASM208733v1_genomic.fna/checkm_input GCF_002087335.1_ASM208733v1_genomic.fna/checkm_result
[2024-01-24 10:48:43,665] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:43,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:43,695] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:43,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:43,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002087335.1_ASM208733v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:43,697] [INFO] Task started: Blastn
[2024-01-24 10:48:43,697] [INFO] Running command: blastn -query GCF_002087335.1_ASM208733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6688de59-c9cc-4ceb-8616-dc24b125f6a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002087335.1_ASM208733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:45,354] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:45,358] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:45,358] [INFO] Target genome list was writen to GCF_002087335.1_ASM208733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:45,367] [INFO] Task started: fastANI
[2024-01-24 10:48:45,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f78205-03de-47eb-ba45-27fe262ec423/GCF_002087335.1_ASM208733v1_genomic.fna.gz --refList GCF_002087335.1_ASM208733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002087335.1_ASM208733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:56,187] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:56,199] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:56,199] [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_002087335.1	s__Pseudophaeobacter leonis	100.0	1527	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000473205.1	s__Pseudophaeobacter arcticus	82.2208	942	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479575.1	s__Pseudophaeobacter sp905479575	81.992	877	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457775.1	s__Pseudophaeobacter sp001457775	81.9837	868	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	81.8076	935	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294455.1	s__Pseudophaeobacter sp001294455	81.4468	902	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.13	98.13	0.97	0.97	2	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	81.4199	897	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152965.1	s__Pseudophaeobacter sp000152965	80.9903	837	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.26	98.26	0.93	0.93	2	-
GCF_000473325.1	s__Leisingera caerulea	78.4977	631	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401945.1	s__Parasedimentitalea sp002401945	78.17	482	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	76.8646	289	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:56,201] [INFO] GTDB search result was written to GCF_002087335.1_ASM208733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:56,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:56,207] [INFO] DFAST_QC result json was written to GCF_002087335.1_ASM208733v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:56,207] [INFO] DFAST_QC completed!
[2024-01-24 10:48:56,207] [INFO] Total running time: 0h1m33s