[2024-01-24 14:39:45,841] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,365] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,365] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2df6c90-7066-467d-ad6f-7ed8a25df807/GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/cds.fna -a GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:54,568] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:54,568] [INFO] Task started: HMMsearch
[2024-01-24 14:39:54,569] [INFO] Running command: hmmsearch --tblout GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference/reference_markers.hmm GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:54,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:54,851] [INFO] Found 6/6 markers.
[2024-01-24 14:39:54,890] [INFO] Query marker FASTA was written to GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:39:54,891] [INFO] Task started: Blastn
[2024-01-24 14:39:54,891] [INFO] Running command: blastn -query GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference/reference_markers.fasta -out GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:55,490] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:55,494] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:55,495] [INFO] Target genome list was writen to GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:39:55,502] [INFO] Task started: fastANI
[2024-01-24 14:39:55,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2df6c90-7066-467d-ad6f-7ed8a25df807/GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna.gz --refList GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:03,270] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:03,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:03,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:03,278] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:03,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:03,278] [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
Salimicrobium jeotgali	strain=MJ3	GCA_000299295.2	1230341	1230341	type	True	97.67	763	842	95	conclusive
Salimicrobium jeotgali	strain=MJ3	GCA_001685435.3	1230341	1230341	type	True	97.645	773	842	95	conclusive
Salimicrobium humidisoli	strain=WN024	GCA_002295105.1	2029857	2029857	type	True	94.6467	775	842	95	below_threshold
Salimicrobium flavidum	strain=DSM 23127	GCA_900156645.1	570947	570947	type	True	78.6888	309	842	95	below_threshold
Salimicrobium halophilum	strain=DSM 4771	GCA_900100295.1	86666	86666	type	True	78.3491	291	842	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	77.1538	50	842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:03,280] [INFO] DFAST Taxonomy check result was written to GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:40:03,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:03,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:03,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference/checkm_data
[2024-01-24 14:40:03,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:03,318] [INFO] Task started: CheckM
[2024-01-24 14:40:03,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/checkm_input GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:40:28,521] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:28,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:28,543] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:28,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:28,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:40:28,545] [INFO] Task started: Blastn
[2024-01-24 14:40:28,545] [INFO] Running command: blastn -query GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg963622dc-a57d-45c0-8098-4814cf881747/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:29,412] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:29,416] [INFO] Selected 21 target genomes.
[2024-01-24 14:40:29,417] [INFO] Target genome list was writen to GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:29,463] [INFO] Task started: fastANI
[2024-01-24 14:40:29,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2df6c90-7066-467d-ad6f-7ed8a25df807/GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna.gz --refList GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:42,039] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:42,049] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:42,049] [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_900107115.1	s__Salimicrobium album	98.6987	780	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	97.70	97.32	0.90	0.88	5	conclusive
GCF_002295105.1	s__Salimicrobium sp002295105	94.624	776	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	98.33	98.33	0.92	0.92	2	-
GCF_900156645.1	s__Salimicrobium flavidum	78.6889	310	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100295.1	s__Salimicrobium halophilum	78.3697	291	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Salimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684905.1	s__Halobacillus salinus	77.4161	56	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.08	98.08	0.93	0.93	2	-
GCF_009856415.1	s__Halobacillus litoralis_C	77.3582	60	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496835.1	s__Thalassobacillus devorans_B	77.331	53	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469135.2	s__Halobacillus sp001592845	76.8314	74	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.23	99.19	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:42,051] [INFO] GTDB search result was written to GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:42,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:42,054] [INFO] DFAST_QC result json was written to GCF_900156705.1_IMG-taxon_2681813520_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:40:42,055] [INFO] DFAST_QC completed!
[2024-01-24 14:40:42,055] [INFO] Total running time: 0h0m56s