[2024-01-24 11:12:48,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference
[2024-01-24 11:12:49,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,906] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg73b08ab4-6bb4-4c44-a6d0-d4705d9d9308/GCF_010634845.1_ASM1063484v1_genomic.fna.gz | prodigal -d GCF_010634845.1_ASM1063484v1_genomic.fna/cds.fna -a GCF_010634845.1_ASM1063484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:14,208] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:14,208] [INFO] Task started: HMMsearch
[2024-01-24 11:13:14,209] [INFO] Running command: hmmsearch --tblout GCF_010634845.1_ASM1063484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference/reference_markers.hmm GCF_010634845.1_ASM1063484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:14,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:14,543] [INFO] Found 6/6 markers.
[2024-01-24 11:13:14,597] [INFO] Query marker FASTA was written to GCF_010634845.1_ASM1063484v1_genomic.fna/markers.fasta
[2024-01-24 11:13:14,598] [INFO] Task started: Blastn
[2024-01-24 11:13:14,598] [INFO] Running command: blastn -query GCF_010634845.1_ASM1063484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference/reference_markers.fasta -out GCF_010634845.1_ASM1063484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,442] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,446] [INFO] Selected 19 target genomes.
[2024-01-24 11:13:15,447] [INFO] Target genome list was writen to GCF_010634845.1_ASM1063484v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:15,601] [INFO] Task started: fastANI
[2024-01-24 11:13:15,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg73b08ab4-6bb4-4c44-a6d0-d4705d9d9308/GCF_010634845.1_ASM1063484v1_genomic.fna.gz --refList GCF_010634845.1_ASM1063484v1_genomic.fna/target_genomes.txt --output GCF_010634845.1_ASM1063484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:43,263] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:43,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:43,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:43,281] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:43,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:43,281] [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
Pseudomonas antarctica	strain=CMS 35	GCA_010634845.1	219572	219572	type	True	100.0	2117	2120	95	conclusive
Pseudomonas antarctica		GCA_900624995.1	219572	219572	type	True	99.8969	1922	2120	95	conclusive
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	89.5577	1684	2120	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	89.4988	1742	2120	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	89.4639	1722	2120	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	88.1538	1491	2120	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.1137	1529	2120	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	88.0918	1544	2120	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.9496	1640	2120	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.8523	1602	2120	95	below_threshold
Pseudomonas palleroniana	strain=LMG 23076	GCA_003031675.1	191390	191390	type	True	87.4434	1565	2120	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	86.7098	1608	2120	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.8784	1463	2120	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	85.857	1405	2120	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.0803	1280	2120	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	80.5499	717	2120	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.106	76	2120	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	75.7584	83	2120	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	75.7503	97	2120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:43,283] [INFO] DFAST Taxonomy check result was written to GCF_010634845.1_ASM1063484v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:43,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:43,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:43,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference/checkm_data
[2024-01-24 11:13:43,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:43,345] [INFO] Task started: CheckM
[2024-01-24 11:13:43,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010634845.1_ASM1063484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010634845.1_ASM1063484v1_genomic.fna/checkm_input GCF_010634845.1_ASM1063484v1_genomic.fna/checkm_result
[2024-01-24 11:14:51,418] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:51,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:51,440] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:51,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:51,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010634845.1_ASM1063484v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:51,441] [INFO] Task started: Blastn
[2024-01-24 11:14:51,442] [INFO] Running command: blastn -query GCF_010634845.1_ASM1063484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f17f7f8-5847-45ee-9b62-c2a16ffa6b42/dqc_reference/reference_markers_gtdb.fasta -out GCF_010634845.1_ASM1063484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:52,820] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:52,824] [INFO] Selected 20 target genomes.
[2024-01-24 11:14:52,824] [INFO] Target genome list was writen to GCF_010634845.1_ASM1063484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:52,843] [INFO] Task started: fastANI
[2024-01-24 11:14:52,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg73b08ab4-6bb4-4c44-a6d0-d4705d9d9308/GCF_010634845.1_ASM1063484v1_genomic.fna.gz --refList GCF_010634845.1_ASM1063484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010634845.1_ASM1063484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:24,507] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:24,529] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:24,529] [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_900624995.1	s__Pseudomonas_E antarctica	99.8969	1922	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	1.00	1.00	3	conclusive
GCF_009707325.1	s__Pseudomonas_E sp002263605	93.1354	1670	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.58	0.94	0.94	2	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	90.8002	1775	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	90.1506	1745	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	89.9191	1754	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_900215245.1	s__Pseudomonas_E fluorescens	89.5053	1741	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_005938045.2	s__Pseudomonas_E sp005938045	88.9929	1710	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.18	95.16	0.86	0.86	3	-
GCF_001050345.1	s__Pseudomonas_E fildesensis	88.3571	1575	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612935.1	s__Pseudomonas_E sp003013355	88.1792	1655	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.56	0.95	0.92	7	-
GCF_007858185.1	s__Pseudomonas_E grimontii	88.1126	1557	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	88.1096	1541	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.28	0.91	0.87	10	-
GCF_009866765.1	s__Pseudomonas_E sp009866765	87.694	1545	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230465.1	s__Pseudomonas_E cremoris	87.6174	1546	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.87	96.78	0.87	0.83	4	-
GCF_003031675.1	s__Pseudomonas_E palleroniana	87.4584	1563	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.94	0.95	0.90	8	-
GCF_013386765.1	s__Pseudomonas_E yamanorum_A	87.0105	1571	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.16	0.94	0.91	5	-
GCF_002204795.1	s__Pseudomonas_E sp002204795	86.8831	1543	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251635.1	s__Pseudomonas_E mandelii_B	86.2927	1230	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105155.1	s__Pseudomonas_E prosekii	83.1799	1232	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	96.34	0.92	0.89	8	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	80.9334	901	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	80.8699	834	2120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:24,531] [INFO] GTDB search result was written to GCF_010634845.1_ASM1063484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:24,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:24,536] [INFO] DFAST_QC result json was written to GCF_010634845.1_ASM1063484v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:24,536] [INFO] DFAST_QC completed!
[2024-01-24 11:15:24,536] [INFO] Total running time: 0h2m36s