[2023-06-29 14:37:25,069] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:37:25,072] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:37:25,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference
[2023-06-29 14:37:26,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:37:26,531] [INFO] Task started: Prodigal
[2023-06-29 14:37:26,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b793207-d89f-433b-a6a5-d954fa7fc101/GCA_023460435.1_ASM2346043v1_genomic.fna.gz | prodigal -d GCA_023460435.1_ASM2346043v1_genomic.fna/cds.fna -a GCA_023460435.1_ASM2346043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:37:35,118] [INFO] Task succeeded: Prodigal
[2023-06-29 14:37:35,118] [INFO] Task started: HMMsearch
[2023-06-29 14:37:35,119] [INFO] Running command: hmmsearch --tblout GCA_023460435.1_ASM2346043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference/reference_markers.hmm GCA_023460435.1_ASM2346043v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:37:35,395] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:37:35,397] [INFO] Found 6/6 markers.
[2023-06-29 14:37:35,446] [INFO] Query marker FASTA was written to GCA_023460435.1_ASM2346043v1_genomic.fna/markers.fasta
[2023-06-29 14:37:35,447] [INFO] Task started: Blastn
[2023-06-29 14:37:35,447] [INFO] Running command: blastn -query GCA_023460435.1_ASM2346043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference/reference_markers.fasta -out GCA_023460435.1_ASM2346043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:37:36,092] [INFO] Task succeeded: Blastn
[2023-06-29 14:37:36,096] [INFO] Selected 14 target genomes.
[2023-06-29 14:37:36,097] [INFO] Target genome list was writen to GCA_023460435.1_ASM2346043v1_genomic.fna/target_genomes.txt
[2023-06-29 14:37:36,098] [INFO] Task started: fastANI
[2023-06-29 14:37:36,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b793207-d89f-433b-a6a5-d954fa7fc101/GCA_023460435.1_ASM2346043v1_genomic.fna.gz --refList GCA_023460435.1_ASM2346043v1_genomic.fna/target_genomes.txt --output GCA_023460435.1_ASM2346043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:37:44,093] [INFO] Task succeeded: fastANI
[2023-06-29 14:37:44,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:37:44,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:37:44,101] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 14:37:44,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 14:37:44,101] [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
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	97.9393	922	1041	95	conclusive
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	77.9065	140	1041	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.0731	111	1041	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	76.9085	96	1041	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	76.8129	91	1041	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:37:44,104] [INFO] DFAST Taxonomy check result was written to GCA_023460435.1_ASM2346043v1_genomic.fna/tc_result.tsv
[2023-06-29 14:37:44,104] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:37:44,105] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:37:44,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference/checkm_data
[2023-06-29 14:37:44,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:37:44,148] [INFO] Task started: CheckM
[2023-06-29 14:37:44,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023460435.1_ASM2346043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023460435.1_ASM2346043v1_genomic.fna/checkm_input GCA_023460435.1_ASM2346043v1_genomic.fna/checkm_result
[2023-06-29 14:38:15,079] [INFO] Task succeeded: CheckM
[2023-06-29 14:38:15,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:38:15,102] [INFO] ===== Completeness check finished =====
[2023-06-29 14:38:15,102] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:38:15,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023460435.1_ASM2346043v1_genomic.fna/markers.fasta)
[2023-06-29 14:38:15,103] [INFO] Task started: Blastn
[2023-06-29 14:38:15,103] [INFO] Running command: blastn -query GCA_023460435.1_ASM2346043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd48d86cc-f1b9-4220-9baa-6e500e47a73b/dqc_reference/reference_markers_gtdb.fasta -out GCA_023460435.1_ASM2346043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:38:15,925] [INFO] Task succeeded: Blastn
[2023-06-29 14:38:15,930] [INFO] Selected 22 target genomes.
[2023-06-29 14:38:15,930] [INFO] Target genome list was writen to GCA_023460435.1_ASM2346043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:38:15,935] [INFO] Task started: fastANI
[2023-06-29 14:38:15,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b793207-d89f-433b-a6a5-d954fa7fc101/GCA_023460435.1_ASM2346043v1_genomic.fna.gz --refList GCA_023460435.1_ASM2346043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023460435.1_ASM2346043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:38:25,278] [INFO] Task succeeded: fastANI
[2023-06-29 14:38:25,290] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:38:25,290] [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_900186535.1	s__Anaerotruncus massiliensis_A	97.9393	922	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.01	98.01	0.87	0.87	2	conclusive
GCF_900078395.1	s__Anaerotruncus rubiinfantis	77.9065	140	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_010206195.1	s__Anaerotruncus colihominis_A	77.24	94	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.98	98.75	0.89	0.87	3	-
GCA_910586875.1	s__Anaerotruncus sp910586875	77.0854	78	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199635.1	s__Anaerotruncus massiliensis	77.0731	111	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_000154565.1	s__Anaerotruncus colihominis	76.9087	95	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	-
GCF_000403395.2	s__Anaerotruncus sp000403395	76.8983	111	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.44	98.36	0.83	0.79	7	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.3094	52	1041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:38:25,292] [INFO] GTDB search result was written to GCA_023460435.1_ASM2346043v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:38:25,292] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:38:25,295] [INFO] DFAST_QC result json was written to GCA_023460435.1_ASM2346043v1_genomic.fna/dqc_result.json
[2023-06-29 14:38:25,296] [INFO] DFAST_QC completed!
[2023-06-29 14:38:25,296] [INFO] Total running time: 0h1m0s