[2024-01-24 11:50:49,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference
[2024-01-24 11:50:50,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,624] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg8375d774-1968-4bdb-97df-10c0adf2cae4/GCF_016918565.1_ASM1691856v1_genomic.fna.gz | prodigal -d GCF_016918565.1_ASM1691856v1_genomic.fna/cds.fna -a GCF_016918565.1_ASM1691856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:04,326] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:04,327] [INFO] Task started: HMMsearch
[2024-01-24 11:51:04,327] [INFO] Running command: hmmsearch --tblout GCF_016918565.1_ASM1691856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference/reference_markers.hmm GCF_016918565.1_ASM1691856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:04,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:04,641] [INFO] Found 6/6 markers.
[2024-01-24 11:51:04,686] [INFO] Query marker FASTA was written to GCF_016918565.1_ASM1691856v1_genomic.fna/markers.fasta
[2024-01-24 11:51:04,687] [INFO] Task started: Blastn
[2024-01-24 11:51:04,687] [INFO] Running command: blastn -query GCF_016918565.1_ASM1691856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference/reference_markers.fasta -out GCF_016918565.1_ASM1691856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:05,254] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:05,257] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:05,257] [INFO] Target genome list was writen to GCF_016918565.1_ASM1691856v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:05,269] [INFO] Task started: fastANI
[2024-01-24 11:51:05,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg8375d774-1968-4bdb-97df-10c0adf2cae4/GCF_016918565.1_ASM1691856v1_genomic.fna.gz --refList GCF_016918565.1_ASM1691856v1_genomic.fna/target_genomes.txt --output GCF_016918565.1_ASM1691856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:17,094] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:17,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:17,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:17,107] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:17,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:17,108] [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
Desulfogranum marinum	strain=DSM 2058	GCA_016918565.1	453220	453220	type	True	100.0	1716	1725	95	conclusive
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	77.3683	145	1725	95	below_threshold
Desulfobulbus rhabdoformis	strain=DSM 8777	GCA_016919065.1	34032	34032	type	True	76.8716	87	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:17,109] [INFO] DFAST Taxonomy check result was written to GCF_016918565.1_ASM1691856v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:17,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:17,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:17,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference/checkm_data
[2024-01-24 11:51:17,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:17,164] [INFO] Task started: CheckM
[2024-01-24 11:51:17,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918565.1_ASM1691856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918565.1_ASM1691856v1_genomic.fna/checkm_input GCF_016918565.1_ASM1691856v1_genomic.fna/checkm_result
[2024-01-24 11:52:00,692] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:00,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,716] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:00,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:00,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918565.1_ASM1691856v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:00,717] [INFO] Task started: Blastn
[2024-01-24 11:52:00,717] [INFO] Running command: blastn -query GCF_016918565.1_ASM1691856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb31dd791-b957-4298-ac0f-759cfecf9719/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918565.1_ASM1691856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:01,438] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:01,442] [INFO] Selected 27 target genomes.
[2024-01-24 11:52:01,443] [INFO] Target genome list was writen to GCF_016918565.1_ASM1691856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:01,468] [INFO] Task started: fastANI
[2024-01-24 11:52:01,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg8375d774-1968-4bdb-97df-10c0adf2cae4/GCF_016918565.1_ASM1691856v1_genomic.fna.gz --refList GCF_016918565.1_ASM1691856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918565.1_ASM1691856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:15,720] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:15,730] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:15,730] [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_016918565.1	s__Desulfobulbus_A marinus	100.0	1716	1725	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002746685.1	s__Desulfobulbus_A propionicus_C	77.4098	75	1725	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429965.1	s__Desulfobulbus_A mediterraneus	77.3701	142	1725	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919065.1	s__Desulfobulbus rhabdoformis	76.8999	86	1725	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748755.1	s__Desulfobulbus_A propionicus_B	76.7649	55	1725	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489765.1	s__DRLX01 sp015489765	76.1073	51	1725	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,732] [INFO] GTDB search result was written to GCF_016918565.1_ASM1691856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:15,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:15,736] [INFO] DFAST_QC result json was written to GCF_016918565.1_ASM1691856v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:15,737] [INFO] DFAST_QC completed!
[2024-01-24 11:52:15,737] [INFO] Total running time: 0h1m26s