[2024-01-24 13:22:00,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference
[2024-01-24 13:22:02,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,019] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg1802018a-5f8f-4bd0-ae4b-0543eff796ea/GCF_005884405.1_ASM588440v1_genomic.fna.gz | prodigal -d GCF_005884405.1_ASM588440v1_genomic.fna/cds.fna -a GCF_005884405.1_ASM588440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:11,519] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:11,520] [INFO] Task started: HMMsearch
[2024-01-24 13:22:11,520] [INFO] Running command: hmmsearch --tblout GCF_005884405.1_ASM588440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference/reference_markers.hmm GCF_005884405.1_ASM588440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:11,794] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:11,796] [INFO] Found 6/6 markers.
[2024-01-24 13:22:11,824] [INFO] Query marker FASTA was written to GCF_005884405.1_ASM588440v1_genomic.fna/markers.fasta
[2024-01-24 13:22:11,824] [INFO] Task started: Blastn
[2024-01-24 13:22:11,824] [INFO] Running command: blastn -query GCF_005884405.1_ASM588440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference/reference_markers.fasta -out GCF_005884405.1_ASM588440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:12,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:12,689] [INFO] Selected 23 target genomes.
[2024-01-24 13:22:12,690] [INFO] Target genome list was writen to GCF_005884405.1_ASM588440v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:12,699] [INFO] Task started: fastANI
[2024-01-24 13:22:12,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg1802018a-5f8f-4bd0-ae4b-0543eff796ea/GCF_005884405.1_ASM588440v1_genomic.fna.gz --refList GCF_005884405.1_ASM588440v1_genomic.fna/target_genomes.txt --output GCF_005884405.1_ASM588440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:27,525] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:27,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:27,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:27,543] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:27,543] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:27,544] [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
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.8301	462	882	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.4259	425	882	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.4016	483	882	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.2063	413	882	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.1345	450	882	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.0891	451	882	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.0286	416	882	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.9764	449	882	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.8778	384	882	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.865	331	882	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.8393	333	882	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.83	420	882	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.7631	407	882	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.7588	405	882	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	78.7481	373	882	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.7159	376	882	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.6729	365	882	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.53	424	882	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.4925	339	882	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	78.2918	291	882	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	78.2876	317	882	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.212	316	882	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	77.6471	215	882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:27,545] [INFO] DFAST Taxonomy check result was written to GCF_005884405.1_ASM588440v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:27,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:27,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:27,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference/checkm_data
[2024-01-24 13:22:27,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:27,579] [INFO] Task started: CheckM
[2024-01-24 13:22:27,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005884405.1_ASM588440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005884405.1_ASM588440v1_genomic.fna/checkm_input GCF_005884405.1_ASM588440v1_genomic.fna/checkm_result
[2024-01-24 13:22:58,838] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:58,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:58,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:58,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:58,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005884405.1_ASM588440v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:58,865] [INFO] Task started: Blastn
[2024-01-24 13:22:58,865] [INFO] Running command: blastn -query GCF_005884405.1_ASM588440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ffdbf83-2c7a-4b3a-b3ab-4c20b3689d42/dqc_reference/reference_markers_gtdb.fasta -out GCF_005884405.1_ASM588440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:00,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:00,099] [INFO] Selected 24 target genomes.
[2024-01-24 13:23:00,099] [INFO] Target genome list was writen to GCF_005884405.1_ASM588440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:00,138] [INFO] Task started: fastANI
[2024-01-24 13:23:00,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg1802018a-5f8f-4bd0-ae4b-0543eff796ea/GCF_005884405.1_ASM588440v1_genomic.fna.gz --refList GCF_005884405.1_ASM588440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005884405.1_ASM588440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:14,696] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:14,716] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:14,716] [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_005884405.1	s__Qipengyuania marisflavi	100.0	881	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016764075.1	s__Qipengyuania sp016764075	79.9409	383	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	79.6572	478	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	79.4378	424	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	79.1871	481	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_011762005.1	s__Qipengyuania flava	79.1451	449	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_009827325.1	s__Qipengyuania vulgaris	79.118	390	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.0334	347	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.9987	439	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355455.1	s__Qipengyuania aurea	78.9976	432	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_009827315.1	s__Qipengyuania gaetbuli	78.9906	447	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.8787	330	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.815	374	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_015767595.1	s__Qipengyuania sp002895025	78.7898	378	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_009828025.1	s__Qipengyuania algicida	78.6779	364	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	78.6397	323	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.53	424	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.4974	318	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.4156	361	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002278985.1	s__34-65-8 sp002278985	78.3408	205	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__34-65-8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	78.3	316	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827495.1	s__Tsuneonella aeria	78.2918	291	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.2295	268	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.1138	353	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:14,718] [INFO] GTDB search result was written to GCF_005884405.1_ASM588440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:14,718] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:14,723] [INFO] DFAST_QC result json was written to GCF_005884405.1_ASM588440v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:14,724] [INFO] DFAST_QC completed!
[2024-01-24 13:23:14,724] [INFO] Total running time: 0h1m14s