[2024-01-25 18:13:35,518] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:35,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:35,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference
[2024-01-25 18:13:36,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:36,708] [INFO] Task started: Prodigal
[2024-01-25 18:13:36,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a7bdcfa-e94b-4e69-9f41-6990a2a814f3/GCF_012985915.1_ASM1298591v1_genomic.fna.gz | prodigal -d GCF_012985915.1_ASM1298591v1_genomic.fna/cds.fna -a GCF_012985915.1_ASM1298591v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:51,830] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:51,830] [INFO] Task started: HMMsearch
[2024-01-25 18:13:51,830] [INFO] Running command: hmmsearch --tblout GCF_012985915.1_ASM1298591v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference/reference_markers.hmm GCF_012985915.1_ASM1298591v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:52,118] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:52,119] [INFO] Found 6/6 markers.
[2024-01-25 18:13:52,168] [INFO] Query marker FASTA was written to GCF_012985915.1_ASM1298591v1_genomic.fna/markers.fasta
[2024-01-25 18:13:52,168] [INFO] Task started: Blastn
[2024-01-25 18:13:52,168] [INFO] Running command: blastn -query GCF_012985915.1_ASM1298591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference/reference_markers.fasta -out GCF_012985915.1_ASM1298591v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:53,194] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:53,198] [INFO] Selected 10 target genomes.
[2024-01-25 18:13:53,198] [INFO] Target genome list was writen to GCF_012985915.1_ASM1298591v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:53,211] [INFO] Task started: fastANI
[2024-01-25 18:13:53,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a7bdcfa-e94b-4e69-9f41-6990a2a814f3/GCF_012985915.1_ASM1298591v1_genomic.fna.gz --refList GCF_012985915.1_ASM1298591v1_genomic.fna/target_genomes.txt --output GCF_012985915.1_ASM1298591v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:06,569] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:06,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:06,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:06,578] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:14:06,579] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:14:06,579] [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 psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	100.0	1944	1987	95	inconclusive
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	99.983	1873	1987	95	inconclusive
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	98.3913	1528	1987	95	inconclusive
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	98.3529	1552	1987	95	inconclusive
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	89.6444	1397	1987	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.5827	712	1987	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	80.4076	696	1987	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.253	648	1987	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	79.9923	662	1987	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	79.6201	587	1987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:06,581] [INFO] DFAST Taxonomy check result was written to GCF_012985915.1_ASM1298591v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:06,582] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:06,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:06,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference/checkm_data
[2024-01-25 18:14:06,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:06,638] [INFO] Task started: CheckM
[2024-01-25 18:14:06,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012985915.1_ASM1298591v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012985915.1_ASM1298591v1_genomic.fna/checkm_input GCF_012985915.1_ASM1298591v1_genomic.fna/checkm_result
[2024-01-25 18:14:52,917] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:52,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:52,942] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:52,942] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:52,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012985915.1_ASM1298591v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:52,942] [INFO] Task started: Blastn
[2024-01-25 18:14:52,943] [INFO] Running command: blastn -query GCF_012985915.1_ASM1298591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83cc95c-1456-4bad-824c-75874bcc3a1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012985915.1_ASM1298591v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:55,073] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:55,082] [INFO] Selected 8 target genomes.
[2024-01-25 18:14:55,082] [INFO] Target genome list was writen to GCF_012985915.1_ASM1298591v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:55,094] [INFO] Task started: fastANI
[2024-01-25 18:14:55,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a7bdcfa-e94b-4e69-9f41-6990a2a814f3/GCF_012985915.1_ASM1298591v1_genomic.fna.gz --refList GCF_012985915.1_ASM1298591v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012985915.1_ASM1298591v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:07,761] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:07,767] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:07,768] [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_000730625.1	s__Pseudomonas_B oryzihabitans	98.3913	1528	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.97	96.38	0.92	0.87	28	conclusive
GCF_014522265.1	s__Pseudomonas_B oryzihabitans_D	93.7044	1519	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	96.63	95.05	0.89	0.84	6	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	93.2251	1533	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_001518815.1	s__Pseudomonas_B oryzihabitans_E	91.092	1424	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_007665395.1	s__Pseudomonas_B psychrotolerans_C	90.8518	1447	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	90.2863	1434	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005250615.1	s__Pseudomonas_B rhizoryzae	89.6537	1397	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.30	97.74	0.93	0.89	15	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	89.4895	1401	1987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:07,769] [INFO] GTDB search result was written to GCF_012985915.1_ASM1298591v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:07,770] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:07,772] [INFO] DFAST_QC result json was written to GCF_012985915.1_ASM1298591v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:07,772] [INFO] DFAST_QC completed!
[2024-01-25 18:15:07,772] [INFO] Total running time: 0h1m32s