[2024-01-24 13:12:51,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:51,247] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:51,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference
[2024-01-24 13:12:52,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:52,567] [INFO] Task started: Prodigal
[2024-01-24 13:12:52,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg86ac9b68-5db9-4c94-9697-8a0647111608/GCF_002844595.1_ASM284459v1_genomic.fna.gz | prodigal -d GCF_002844595.1_ASM284459v1_genomic.fna/cds.fna -a GCF_002844595.1_ASM284459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:05,963] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:05,963] [INFO] Task started: HMMsearch
[2024-01-24 13:13:05,964] [INFO] Running command: hmmsearch --tblout GCF_002844595.1_ASM284459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference/reference_markers.hmm GCF_002844595.1_ASM284459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:06,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:06,333] [INFO] Found 6/6 markers.
[2024-01-24 13:13:06,373] [INFO] Query marker FASTA was written to GCF_002844595.1_ASM284459v1_genomic.fna/markers.fasta
[2024-01-24 13:13:06,374] [INFO] Task started: Blastn
[2024-01-24 13:13:06,374] [INFO] Running command: blastn -query GCF_002844595.1_ASM284459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference/reference_markers.fasta -out GCF_002844595.1_ASM284459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:07,482] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:07,486] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:07,486] [INFO] Target genome list was writen to GCF_002844595.1_ASM284459v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:07,492] [INFO] Task started: fastANI
[2024-01-24 13:13:07,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ac9b68-5db9-4c94-9697-8a0647111608/GCF_002844595.1_ASM284459v1_genomic.fna.gz --refList GCF_002844595.1_ASM284459v1_genomic.fna/target_genomes.txt --output GCF_002844595.1_ASM284459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:19,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:19,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:19,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:19,481] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:19,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:19,482] [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
Pleomorphomonas diazotrophica	strain=R5-392	GCA_002844595.1	1166257	1166257	type	True	100.0	1487	1491	95	conclusive
Pleomorphomonas diazotrophica	strain=R5-392	GCA_900114935.1	1166257	1166257	type	True	99.9958	1486	1491	95	conclusive
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	87.6494	1175	1491	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	86.2949	1060	1491	95	below_threshold
Pleomorphomonas oryzae	strain=DSM 16300	GCA_000422965.1	261934	261934	type	True	85.9148	1216	1491	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.671	362	1491	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.4594	223	1491	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.4123	281	1491	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.8663	346	1491	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.7024	347	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:19,483] [INFO] DFAST Taxonomy check result was written to GCF_002844595.1_ASM284459v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:19,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:19,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:19,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference/checkm_data
[2024-01-24 13:13:19,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:19,533] [INFO] Task started: CheckM
[2024-01-24 13:13:19,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002844595.1_ASM284459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002844595.1_ASM284459v1_genomic.fna/checkm_input GCF_002844595.1_ASM284459v1_genomic.fna/checkm_result
[2024-01-24 13:14:01,270] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:01,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:01,291] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:01,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:01,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002844595.1_ASM284459v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:01,292] [INFO] Task started: Blastn
[2024-01-24 13:14:01,293] [INFO] Running command: blastn -query GCF_002844595.1_ASM284459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba86cb42-3456-4b05-8613-db8fd1990bad/dqc_reference/reference_markers_gtdb.fasta -out GCF_002844595.1_ASM284459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:03,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:03,327] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:03,327] [INFO] Target genome list was writen to GCF_002844595.1_ASM284459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:03,354] [INFO] Task started: fastANI
[2024-01-24 13:14:03,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ac9b68-5db9-4c94-9697-8a0647111608/GCF_002844595.1_ASM284459v1_genomic.fna.gz --refList GCF_002844595.1_ASM284459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002844595.1_ASM284459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:13,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,637] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:13,637] [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_002844595.1	s__Pleomorphomonas diazotrophica	100.0	1487	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	87.6507	1175	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_000425185.1	s__Pleomorphomonas koreensis	86.3061	1059	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCF_000422965.1	s__Pleomorphomonas oryzae	85.8886	1219	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759535.1	s__Pleomorphomonas sp011759535	85.7999	1247	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018262575.1	s__Pleomorphomonas sp018262575	85.5741	1028	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262505.1	s__Pleomorphomonas sp018262505	85.294	1073	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366315.1	s__Pleomorphomonas sp004366315	83.7635	1126	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,639] [INFO] GTDB search result was written to GCF_002844595.1_ASM284459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:13,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:13,644] [INFO] DFAST_QC result json was written to GCF_002844595.1_ASM284459v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:13,644] [INFO] DFAST_QC completed!
[2024-01-24 13:14:13,644] [INFO] Total running time: 0h1m22s