[2024-01-24 13:17:59,125] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:59,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:59,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference
[2024-01-24 13:18:00,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,522] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e0e2601-6583-4170-b61b-f284c2fb4038/GCF_000833025.1_ASM83302v1_genomic.fna.gz | prodigal -d GCF_000833025.1_ASM83302v1_genomic.fna/cds.fna -a GCF_000833025.1_ASM83302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:12,247] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:12,247] [INFO] Task started: HMMsearch
[2024-01-24 13:18:12,248] [INFO] Running command: hmmsearch --tblout GCF_000833025.1_ASM83302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference/reference_markers.hmm GCF_000833025.1_ASM83302v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:12,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:12,565] [INFO] Found 6/6 markers.
[2024-01-24 13:18:12,605] [INFO] Query marker FASTA was written to GCF_000833025.1_ASM83302v1_genomic.fna/markers.fasta
[2024-01-24 13:18:12,605] [INFO] Task started: Blastn
[2024-01-24 13:18:12,606] [INFO] Running command: blastn -query GCF_000833025.1_ASM83302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference/reference_markers.fasta -out GCF_000833025.1_ASM83302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:13,269] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:13,272] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:13,273] [INFO] Target genome list was writen to GCF_000833025.1_ASM83302v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:13,279] [INFO] Task started: fastANI
[2024-01-24 13:18:13,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0e2601-6583-4170-b61b-f284c2fb4038/GCF_000833025.1_ASM83302v1_genomic.fna.gz --refList GCF_000833025.1_ASM83302v1_genomic.fna/target_genomes.txt --output GCF_000833025.1_ASM83302v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:20,834] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:20,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:20,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:20,846] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:20,847] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:20,847] [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
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	100.0	1354	1354	95	inconclusive
Myroides profundi	strain=DSM 19823	GCA_900111065.1	480520	480520	type	True	99.9801	1316	1354	95	inconclusive
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	95.0161	1190	1354	95	inconclusive
Myroides odoratimimus	strain=NCTC11180	GCA_900453765.1	76832	76832	type	True	94.9986	1162	1354	95	below_threshold
Myroides odoratimimus	strain=CCUG39352	GCA_001485415.1	76832	76832	type	True	94.9032	1153	1354	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	83.2826	909	1354	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.8391	123	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,848] [INFO] DFAST Taxonomy check result was written to GCF_000833025.1_ASM83302v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:20,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:20,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:20,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference/checkm_data
[2024-01-24 13:18:20,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:20,901] [INFO] Task started: CheckM
[2024-01-24 13:18:20,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000833025.1_ASM83302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000833025.1_ASM83302v1_genomic.fna/checkm_input GCF_000833025.1_ASM83302v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,064] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,087] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000833025.1_ASM83302v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,088] [INFO] Task started: Blastn
[2024-01-24 13:19:00,088] [INFO] Running command: blastn -query GCF_000833025.1_ASM83302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4664a4e6-c6bc-413a-a2ec-8a0fb037df56/dqc_reference/reference_markers_gtdb.fasta -out GCF_000833025.1_ASM83302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,007] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:01,008] [INFO] Target genome list was writen to GCF_000833025.1_ASM83302v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,020] [INFO] Task started: fastANI
[2024-01-24 13:19:01,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0e2601-6583-4170-b61b-f284c2fb4038/GCF_000833025.1_ASM83302v1_genomic.fna.gz --refList GCF_000833025.1_ASM83302v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000833025.1_ASM83302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:07,119] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,133] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:07,133] [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_000833025.1	s__Flavobacterium profundi	100.0	1354	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001485415.1	s__Flavobacterium odoratimimum	94.9117	1152	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_900109075.1	s__Flavobacterium marinum_A	83.2788	910	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_002286775.1	s__Flavobacterium sp002286775	82.6087	870	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711045.1	s__Flavobacterium album_A	81.2772	479	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.30	99.30	0.90	0.90	2	-
GCF_009799805.1	s__Flavobacterium phaeum_A	80.086	487	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454195.1	s__Flavobacterium sp002454195	77.0832	60	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:07,135] [INFO] GTDB search result was written to GCF_000833025.1_ASM83302v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:07,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:07,138] [INFO] DFAST_QC result json was written to GCF_000833025.1_ASM83302v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:07,138] [INFO] DFAST_QC completed!
[2024-01-24 13:19:07,138] [INFO] Total running time: 0h1m8s