[2024-01-24 11:20:34,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference
[2024-01-24 11:20:35,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,327] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d46dc70-b809-4a80-a1c1-db6865cbd598/GCF_004340125.1_ASM434012v1_genomic.fna.gz | prodigal -d GCF_004340125.1_ASM434012v1_genomic.fna/cds.fna -a GCF_004340125.1_ASM434012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:43,695] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:43,696] [INFO] Task started: HMMsearch
[2024-01-24 11:20:43,696] [INFO] Running command: hmmsearch --tblout GCF_004340125.1_ASM434012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference/reference_markers.hmm GCF_004340125.1_ASM434012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:43,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:43,962] [INFO] Found 6/6 markers.
[2024-01-24 11:20:43,988] [INFO] Query marker FASTA was written to GCF_004340125.1_ASM434012v1_genomic.fna/markers.fasta
[2024-01-24 11:20:43,989] [INFO] Task started: Blastn
[2024-01-24 11:20:43,989] [INFO] Running command: blastn -query GCF_004340125.1_ASM434012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference/reference_markers.fasta -out GCF_004340125.1_ASM434012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:44,767] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:44,771] [INFO] Selected 16 target genomes.
[2024-01-24 11:20:44,772] [INFO] Target genome list was writen to GCF_004340125.1_ASM434012v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:44,785] [INFO] Task started: fastANI
[2024-01-24 11:20:44,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d46dc70-b809-4a80-a1c1-db6865cbd598/GCF_004340125.1_ASM434012v1_genomic.fna.gz --refList GCF_004340125.1_ASM434012v1_genomic.fna/target_genomes.txt --output GCF_004340125.1_ASM434012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:52,936] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:52,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:52,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:52,947] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:52,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:52,947] [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
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	98.7551	897	967	95	conclusive
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	78.2421	147	967	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.8765	204	967	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	77.6347	147	967	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	77.3806	70	967	95	below_threshold
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	77.2779	80	967	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.9506	57	967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:52,948] [INFO] DFAST Taxonomy check result was written to GCF_004340125.1_ASM434012v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:52,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:52,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:52,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference/checkm_data
[2024-01-24 11:20:52,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:52,978] [INFO] Task started: CheckM
[2024-01-24 11:20:52,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340125.1_ASM434012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340125.1_ASM434012v1_genomic.fna/checkm_input GCF_004340125.1_ASM434012v1_genomic.fna/checkm_result
[2024-01-24 11:21:21,197] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:21,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:21,216] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:21,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:21,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340125.1_ASM434012v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:21,218] [INFO] Task started: Blastn
[2024-01-24 11:21:21,218] [INFO] Running command: blastn -query GCF_004340125.1_ASM434012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e5f2b59-9472-483f-8e08-e3ae3c729899/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340125.1_ASM434012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:22,615] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:22,619] [INFO] Selected 19 target genomes.
[2024-01-24 11:21:22,619] [INFO] Target genome list was writen to GCF_004340125.1_ASM434012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:22,642] [INFO] Task started: fastANI
[2024-01-24 11:21:22,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d46dc70-b809-4a80-a1c1-db6865cbd598/GCF_004340125.1_ASM434012v1_genomic.fna.gz --refList GCF_004340125.1_ASM434012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340125.1_ASM434012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:30,474] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:30,491] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:30,491] [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
GCA_004340125.1	s__Harryflintia acetispora	100.0	967	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	conclusive
GCF_001486165.1	s__Bittarella massiliensis	78.2423	147	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Bittarella	95.0	97.23	96.02	0.88	0.84	8	-
GCF_017566145.1	s__Bittarella massiliensis_A	77.9464	137	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Bittarella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160895.1	s__Faecalibacterium sp002160895	77.9423	83	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.38	97.36	0.82	0.81	3	-
GCF_900199635.1	s__Anaerotruncus massiliensis	77.834	206	967	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_904419105.1	s__Avimicrobium faecavium	77.5434	77	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385095.1	s__Pararuminococcus sp014385095	77.2169	138	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pararuminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716285.1	s__Merdivicinus faecavium	77.0579	112	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	99.37	98.77	0.95	0.93	3	-
GCF_904398325.1	s__Neoruminococcus faecicola	77.0094	90	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585525.1	s__Angelakisella sp910585525	76.7794	116	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113125.1	s__Pygmaiobacter gallistercoris	76.6596	66	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pygmaiobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.618	93	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCA_019116585.1	s__Faecalibacterium gallistercoris	76.5154	76	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.23	98.17	0.89	0.87	6	-
GCA_019119685.1	s__Faecalibacterium faecigallinarum	76.1663	69	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.44	97.44	0.75	0.75	2	-
GCA_900546265.1	s__UMGS856 sp900546265	76.1563	86	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856	95.0	99.40	99.16	0.90	0.87	3	-
GCA_019113345.1	s__Faecalibacterium intestinigallinarum	76.034	75	967	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.07	98.05	0.85	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:30,493] [INFO] GTDB search result was written to GCF_004340125.1_ASM434012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:30,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:30,496] [INFO] DFAST_QC result json was written to GCF_004340125.1_ASM434012v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:30,496] [INFO] DFAST_QC completed!
[2024-01-24 11:21:30,496] [INFO] Total running time: 0h0m56s