[2024-01-24 13:24:12,457] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,459] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference
[2024-01-24 13:24:13,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,714] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg9db4aee9-85bb-473b-a671-23c864d9a2f3/GCF_016028655.1_ASM1602865v1_genomic.fna.gz | prodigal -d GCF_016028655.1_ASM1602865v1_genomic.fna/cds.fna -a GCF_016028655.1_ASM1602865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:27,135] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:27,135] [INFO] Task started: HMMsearch
[2024-01-24 13:24:27,135] [INFO] Running command: hmmsearch --tblout GCF_016028655.1_ASM1602865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference/reference_markers.hmm GCF_016028655.1_ASM1602865v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:27,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:27,350] [INFO] Found 6/6 markers.
[2024-01-24 13:24:27,387] [INFO] Query marker FASTA was written to GCF_016028655.1_ASM1602865v1_genomic.fna/markers.fasta
[2024-01-24 13:24:27,387] [INFO] Task started: Blastn
[2024-01-24 13:24:27,387] [INFO] Running command: blastn -query GCF_016028655.1_ASM1602865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference/reference_markers.fasta -out GCF_016028655.1_ASM1602865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:28,381] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:28,384] [INFO] Selected 12 target genomes.
[2024-01-24 13:24:28,384] [INFO] Target genome list was writen to GCF_016028655.1_ASM1602865v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:28,398] [INFO] Task started: fastANI
[2024-01-24 13:24:28,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db4aee9-85bb-473b-a671-23c864d9a2f3/GCF_016028655.1_ASM1602865v1_genomic.fna.gz --refList GCF_016028655.1_ASM1602865v1_genomic.fna/target_genomes.txt --output GCF_016028655.1_ASM1602865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:40,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:40,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:40,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:40,541] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:24:40,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:40,542] [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
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	100.0	1511	1511	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	99.9893	1510	1511	95	conclusive
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	91.2232	1266	1511	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	91.1651	1241	1511	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	91.1609	1245	1511	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	89.2	1224	1511	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	89.1364	1213	1511	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	87.6845	1250	1511	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	87.6241	1249	1511	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.2399	939	1511	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	82.8307	920	1511	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	81.2552	672	1511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:40,543] [INFO] DFAST Taxonomy check result was written to GCF_016028655.1_ASM1602865v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:40,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:40,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:40,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference/checkm_data
[2024-01-24 13:24:40,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:40,603] [INFO] Task started: CheckM
[2024-01-24 13:24:40,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028655.1_ASM1602865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028655.1_ASM1602865v1_genomic.fna/checkm_input GCF_016028655.1_ASM1602865v1_genomic.fna/checkm_result
[2024-01-24 13:25:21,785] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:21,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:21,804] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:21,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:21,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028655.1_ASM1602865v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:21,805] [INFO] Task started: Blastn
[2024-01-24 13:25:21,805] [INFO] Running command: blastn -query GCF_016028655.1_ASM1602865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ea5b085-b1ac-4dcd-bd0d-e0dbb0c69e06/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028655.1_ASM1602865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:23,683] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:23,686] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:23,686] [INFO] Target genome list was writen to GCF_016028655.1_ASM1602865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:23,701] [INFO] Task started: fastANI
[2024-01-24 13:25:23,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db4aee9-85bb-473b-a671-23c864d9a2f3/GCF_016028655.1_ASM1602865v1_genomic.fna.gz --refList GCF_016028655.1_ASM1602865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028655.1_ASM1602865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:38,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:38,206] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:38,206] [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_000219605.1	s__Pseudomonas_A stutzeri	99.9893	1510	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	conclusive
GCF_003205815.1	s__Pseudomonas_A sp003205815	90.7318	1250	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	89.2	1224	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	88.0322	1208	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	87.9651	1204	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	87.8439	1251	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	87.8122	1248	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	87.7484	1263	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0711	97.19	97.19	0.89	0.89	2	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	87.733	1248	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.44	99.44	0.92	0.92	2	-
GCF_900114065.1	s__Pseudomonas_A kunmingensis	87.6969	1248	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.31	97.18	0.87	0.86	3	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	87.6594	1157	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	87.2096	1130	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	86.719	1187	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	86.1546	1079	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:38,208] [INFO] GTDB search result was written to GCF_016028655.1_ASM1602865v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:38,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:38,211] [INFO] DFAST_QC result json was written to GCF_016028655.1_ASM1602865v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:38,212] [INFO] DFAST_QC completed!
[2024-01-24 13:25:38,212] [INFO] Total running time: 0h1m26s