[2023-06-28 13:30:21,304] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:30:21,309] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:30:21,309] [INFO] DQC Reference Directory: /var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference
[2023-06-28 13:30:22,551] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:30:22,552] [INFO] Task started: Prodigal
[2023-06-28 13:30:22,552] [INFO] Running command: gunzip -c /var/lib/cwl/stge380e45d-3e5d-4336-b5c2-2a80cde92031/GCA_020354435.1_ASM2035443v1_genomic.fna.gz | prodigal -d GCA_020354435.1_ASM2035443v1_genomic.fna/cds.fna -a GCA_020354435.1_ASM2035443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:30:32,950] [INFO] Task succeeded: Prodigal
[2023-06-28 13:30:32,951] [INFO] Task started: HMMsearch
[2023-06-28 13:30:32,951] [INFO] Running command: hmmsearch --tblout GCA_020354435.1_ASM2035443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference/reference_markers.hmm GCA_020354435.1_ASM2035443v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:30:33,237] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:30:33,239] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge380e45d-3e5d-4336-b5c2-2a80cde92031/GCA_020354435.1_ASM2035443v1_genomic.fna.gz]
[2023-06-28 13:30:33,274] [INFO] Query marker FASTA was written to GCA_020354435.1_ASM2035443v1_genomic.fna/markers.fasta
[2023-06-28 13:30:33,275] [INFO] Task started: Blastn
[2023-06-28 13:30:33,275] [INFO] Running command: blastn -query GCA_020354435.1_ASM2035443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference/reference_markers.fasta -out GCA_020354435.1_ASM2035443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:34,001] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:34,005] [INFO] Selected 29 target genomes.
[2023-06-28 13:30:34,006] [INFO] Target genome list was writen to GCA_020354435.1_ASM2035443v1_genomic.fna/target_genomes.txt
[2023-06-28 13:30:34,008] [INFO] Task started: fastANI
[2023-06-28 13:30:34,008] [INFO] Running command: fastANI --query /var/lib/cwl/stge380e45d-3e5d-4336-b5c2-2a80cde92031/GCA_020354435.1_ASM2035443v1_genomic.fna.gz --refList GCA_020354435.1_ASM2035443v1_genomic.fna/target_genomes.txt --output GCA_020354435.1_ASM2035443v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:30:51,514] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:51,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:30:51,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:30:51,531] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:30:51,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:30:51,532] [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
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.0393	51	1240	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.0178	56	1240	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.9177	55	1240	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	75.6993	55	1240	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.6161	70	1240	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	75.5889	57	1240	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	75.4779	55	1240	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	75.4408	51	1240	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.3608	51	1240	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	75.2608	52	1240	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	75.2599	68	1240	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	75.1652	55	1240	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:30:51,534] [INFO] DFAST Taxonomy check result was written to GCA_020354435.1_ASM2035443v1_genomic.fna/tc_result.tsv
[2023-06-28 13:30:51,535] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:30:51,535] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:30:51,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference/checkm_data
[2023-06-28 13:30:51,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:30:51,575] [INFO] Task started: CheckM
[2023-06-28 13:30:51,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020354435.1_ASM2035443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020354435.1_ASM2035443v1_genomic.fna/checkm_input GCA_020354435.1_ASM2035443v1_genomic.fna/checkm_result
[2023-06-28 13:31:25,450] [INFO] Task succeeded: CheckM
[2023-06-28 13:31:25,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:31:25,471] [INFO] ===== Completeness check finished =====
[2023-06-28 13:31:25,471] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:31:25,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020354435.1_ASM2035443v1_genomic.fna/markers.fasta)
[2023-06-28 13:31:25,472] [INFO] Task started: Blastn
[2023-06-28 13:31:25,472] [INFO] Running command: blastn -query GCA_020354435.1_ASM2035443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1cbb2bd-b945-49e7-978a-93bc5ec9c9bc/dqc_reference/reference_markers_gtdb.fasta -out GCA_020354435.1_ASM2035443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:26,614] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:26,619] [INFO] Selected 20 target genomes.
[2023-06-28 13:31:26,620] [INFO] Target genome list was writen to GCA_020354435.1_ASM2035443v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:31:26,630] [INFO] Task started: fastANI
[2023-06-28 13:31:26,631] [INFO] Running command: fastANI --query /var/lib/cwl/stge380e45d-3e5d-4336-b5c2-2a80cde92031/GCA_020354435.1_ASM2035443v1_genomic.fna.gz --refList GCA_020354435.1_ASM2035443v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020354435.1_ASM2035443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:31:39,461] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:39,480] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:31:39,480] [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_009937625.1	s__GCA-001735895 sp009937625	79.8121	612	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001735895.1	s__GCA-001735895 sp001735895	78.8221	485	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494335.1	s__S144-22 sp015494335	77.0082	113	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__S144-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231795.1	s__GCA-001735895 sp003231795	76.579	106	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003645435.1	s__GCA-001735895 sp003645435	76.5252	89	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712635.1	s__JADJWH01 sp016712635	76.3922	59	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	76.3771	62	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCA_011371465.1	s__Thiogranum sp011371465	75.9471	55	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584085.1	s__Halochromatium glycolicum	75.9177	55	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	75.7251	60	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCA_014382695.1	s__JACNJF01 sp014382695	75.7078	54	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__JACNJF01	95.0	99.61	99.61	0.86	0.86	2	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.5052	90	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_012767755.2	s__Pseudomonas_F sp003234055	75.3859	74	1240	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-28 13:31:39,482] [INFO] GTDB search result was written to GCA_020354435.1_ASM2035443v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:31:39,482] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:31:39,486] [INFO] DFAST_QC result json was written to GCA_020354435.1_ASM2035443v1_genomic.fna/dqc_result.json
[2023-06-28 13:31:39,486] [INFO] DFAST_QC completed!
[2023-06-28 13:31:39,486] [INFO] Total running time: 0h1m18s