[2024-01-24 12:23:03,728] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,731] [INFO] DQC Reference Directory: /var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference
[2024-01-24 12:23:05,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,039] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bfb01d5-9e85-4f55-9bf3-809a37df85ce/GCF_016919005.1_ASM1691900v1_genomic.fna.gz | prodigal -d GCF_016919005.1_ASM1691900v1_genomic.fna/cds.fna -a GCF_016919005.1_ASM1691900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:18,516] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:18,516] [INFO] Task started: HMMsearch
[2024-01-24 12:23:18,517] [INFO] Running command: hmmsearch --tblout GCF_016919005.1_ASM1691900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference/reference_markers.hmm GCF_016919005.1_ASM1691900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:18,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:18,917] [INFO] Found 6/6 markers.
[2024-01-24 12:23:18,967] [INFO] Query marker FASTA was written to GCF_016919005.1_ASM1691900v1_genomic.fna/markers.fasta
[2024-01-24 12:23:18,967] [INFO] Task started: Blastn
[2024-01-24 12:23:18,968] [INFO] Running command: blastn -query GCF_016919005.1_ASM1691900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference/reference_markers.fasta -out GCF_016919005.1_ASM1691900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,577] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,581] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:19,581] [INFO] Target genome list was writen to GCF_016919005.1_ASM1691900v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:19,589] [INFO] Task started: fastANI
[2024-01-24 12:23:19,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bfb01d5-9e85-4f55-9bf3-809a37df85ce/GCF_016919005.1_ASM1691900v1_genomic.fna.gz --refList GCF_016919005.1_ASM1691900v1_genomic.fna/target_genomes.txt --output GCF_016919005.1_ASM1691900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:32,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:32,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:32,852] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:32,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:32,853] [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
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	76.7821	82	1612	95	below_threshold
Desulforhopalus singaporensis	strain=DSM 12130	GCA_900104445.1	91360	91360	type	True	76.4075	71	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:32,855] [INFO] DFAST Taxonomy check result was written to GCF_016919005.1_ASM1691900v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:32,856] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:32,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:32,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference/checkm_data
[2024-01-24 12:23:32,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:32,909] [INFO] Task started: CheckM
[2024-01-24 12:23:32,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016919005.1_ASM1691900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016919005.1_ASM1691900v1_genomic.fna/checkm_input GCF_016919005.1_ASM1691900v1_genomic.fna/checkm_result
[2024-01-24 12:24:15,295] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:15,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,320] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:15,320] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:15,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016919005.1_ASM1691900v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:15,321] [INFO] Task started: Blastn
[2024-01-24 12:24:15,321] [INFO] Running command: blastn -query GCF_016919005.1_ASM1691900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga24730d4-17c5-47b2-b8ca-310d46147c46/dqc_reference/reference_markers_gtdb.fasta -out GCF_016919005.1_ASM1691900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:16,081] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:16,086] [INFO] Selected 28 target genomes.
[2024-01-24 12:24:16,086] [INFO] Target genome list was writen to GCF_016919005.1_ASM1691900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:16,128] [INFO] Task started: fastANI
[2024-01-24 12:24:16,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bfb01d5-9e85-4f55-9bf3-809a37df85ce/GCF_016919005.1_ASM1691900v1_genomic.fna.gz --refList GCF_016919005.1_ASM1691900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016919005.1_ASM1691900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:35,443] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:35,454] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:35,454] [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_016919005.1	s__Desulfopila_A inferna	100.0	1611	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila_A	95.0	95.27	95.27	0.87	0.87	2	conclusive
GCA_000961725.1	s__Desulforhopalus sp000961725	77.0312	128	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143695.1	s__Desulfopila aestuarii	76.8016	82	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352445.1	s__Desulforhopalus sp002352445	76.5357	50	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875445.1	s__Desulforhopalus sp903875445	76.5101	85	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	99.93	99.88	0.93	0.87	5	-
GCA_903901335.1	s__CAIUQR01 sp903901335	76.4391	80	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__CAIUQR01	95.0	99.73	99.56	0.92	0.89	4	-
GCF_900104445.1	s__Desulforhopalus singaporensis	76.4135	72	1612	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:35,456] [INFO] GTDB search result was written to GCF_016919005.1_ASM1691900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:35,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:35,459] [INFO] DFAST_QC result json was written to GCF_016919005.1_ASM1691900v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:35,459] [INFO] DFAST_QC completed!
[2024-01-24 12:24:35,459] [INFO] Total running time: 0h1m32s