[2023-06-27 00:32:42,010] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:32:42,039] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:32:42,040] [INFO] DQC Reference Directory: /var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference
[2023-06-27 00:32:43,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:32:43,332] [INFO] Task started: Prodigal
[2023-06-27 00:32:43,332] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd88d692-91fa-465f-a764-0e9758b25c0b/GCA_002280035.1_ASM228003v1_genomic.fna.gz | prodigal -d GCA_002280035.1_ASM228003v1_genomic.fna/cds.fna -a GCA_002280035.1_ASM228003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:32:48,803] [INFO] Task succeeded: Prodigal
[2023-06-27 00:32:48,804] [INFO] Task started: HMMsearch
[2023-06-27 00:32:48,804] [INFO] Running command: hmmsearch --tblout GCA_002280035.1_ASM228003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference/reference_markers.hmm GCA_002280035.1_ASM228003v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:32:49,040] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:32:49,042] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbd88d692-91fa-465f-a764-0e9758b25c0b/GCA_002280035.1_ASM228003v1_genomic.fna.gz]
[2023-06-27 00:32:49,105] [INFO] Query marker FASTA was written to GCA_002280035.1_ASM228003v1_genomic.fna/markers.fasta
[2023-06-27 00:32:49,106] [INFO] Task started: Blastn
[2023-06-27 00:32:49,106] [INFO] Running command: blastn -query GCA_002280035.1_ASM228003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference/reference_markers.fasta -out GCA_002280035.1_ASM228003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:32:49,819] [INFO] Task succeeded: Blastn
[2023-06-27 00:32:49,823] [INFO] Selected 18 target genomes.
[2023-06-27 00:32:49,823] [INFO] Target genome list was writen to GCA_002280035.1_ASM228003v1_genomic.fna/target_genomes.txt
[2023-06-27 00:32:49,837] [INFO] Task started: fastANI
[2023-06-27 00:32:49,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd88d692-91fa-465f-a764-0e9758b25c0b/GCA_002280035.1_ASM228003v1_genomic.fna.gz --refList GCA_002280035.1_ASM228003v1_genomic.fna/target_genomes.txt --output GCA_002280035.1_ASM228003v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:33:01,825] [INFO] Task succeeded: fastANI
[2023-06-27 00:33:01,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:33:01,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:33:01,841] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 00:33:01,841] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 00:33:01,841] [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 saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	84.6973	129	168	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.3596	122	168	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	82.4436	119	168	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	82.4324	118	168	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	81.9626	110	168	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	81.9586	109	168	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	81.9586	109	168	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	81.935	103	168	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	81.9067	103	168	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	81.0798	106	168	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	81.0533	108	168	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	80.8294	101	168	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.8027	66	168	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	80.3209	85	168	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	80.1831	70	168	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	80.0742	97	168	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	79.8124	79	168	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	79.745	85	168	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:33:01,843] [INFO] DFAST Taxonomy check result was written to GCA_002280035.1_ASM228003v1_genomic.fna/tc_result.tsv
[2023-06-27 00:33:01,844] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:33:01,844] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:33:01,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference/checkm_data
[2023-06-27 00:33:01,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:33:01,877] [INFO] Task started: CheckM
[2023-06-27 00:33:01,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002280035.1_ASM228003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002280035.1_ASM228003v1_genomic.fna/checkm_input GCA_002280035.1_ASM228003v1_genomic.fna/checkm_result
[2023-06-27 00:33:24,996] [INFO] Task succeeded: CheckM
[2023-06-27 00:33:24,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.63%
Contamintation: 1.52%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-27 00:33:25,024] [INFO] ===== Completeness check finished =====
[2023-06-27 00:33:25,024] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:33:25,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002280035.1_ASM228003v1_genomic.fna/markers.fasta)
[2023-06-27 00:33:25,025] [INFO] Task started: Blastn
[2023-06-27 00:33:25,025] [INFO] Running command: blastn -query GCA_002280035.1_ASM228003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4fdc117-3154-4e84-9e02-4139b5a89077/dqc_reference/reference_markers_gtdb.fasta -out GCA_002280035.1_ASM228003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:33:26,085] [INFO] Task succeeded: Blastn
[2023-06-27 00:33:26,089] [INFO] Selected 9 target genomes.
[2023-06-27 00:33:26,090] [INFO] Target genome list was writen to GCA_002280035.1_ASM228003v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:33:26,098] [INFO] Task started: fastANI
[2023-06-27 00:33:26,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd88d692-91fa-465f-a764-0e9758b25c0b/GCA_002280035.1_ASM228003v1_genomic.fna.gz --refList GCA_002280035.1_ASM228003v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002280035.1_ASM228003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:33:32,077] [INFO] Task succeeded: fastANI
[2023-06-27 00:33:32,144] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 00:33:32,145] [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
GCA_002331645.1	s__Pseudomonas_A stutzeri_T	98.091	142	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.46	98.46	0.92	0.92	2	conclusive
GCF_013522825.1	s__Pseudomonas_A stutzeri_AK	88.417	143	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345575.1	s__Pseudomonas_A stutzeri_S	85.3773	138	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756775.1	s__Pseudomonas_A saudiphocaensis	84.6973	129	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.10	98.10	0.92	0.90	3	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	82.1798	122	168	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_004331835.1	s__Pseudomonas_A sp004331835	81.7094	112	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.93	97.83	0.93	0.91	3	-
GCA_002339675.1	s__Pseudomonas_A stutzeri_O	81.2777	113	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090095.1	s__Pseudomonas_A stutzeri_AN	81.1859	106	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	80.9567	104	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 00:33:32,147] [INFO] GTDB search result was written to GCA_002280035.1_ASM228003v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:33:32,148] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:33:32,187] [INFO] DFAST_QC result json was written to GCA_002280035.1_ASM228003v1_genomic.fna/dqc_result.json
[2023-06-27 00:33:32,187] [INFO] DFAST_QC completed!
[2023-06-27 00:33:32,187] [INFO] Total running time: 0h0m50s