[2024-01-24 11:58:57,248] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,251] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference
[2024-01-24 11:58:58,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,687] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cd2b89c-5c78-47e6-a817-48c9d9ece60d/GCF_005280655.1_ASM528065v1_genomic.fna.gz | prodigal -d GCF_005280655.1_ASM528065v1_genomic.fna/cds.fna -a GCF_005280655.1_ASM528065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:08,329] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:08,329] [INFO] Task started: HMMsearch
[2024-01-24 11:59:08,329] [INFO] Running command: hmmsearch --tblout GCF_005280655.1_ASM528065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference/reference_markers.hmm GCF_005280655.1_ASM528065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:08,646] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:08,647] [INFO] Found 6/6 markers.
[2024-01-24 11:59:08,707] [INFO] Query marker FASTA was written to GCF_005280655.1_ASM528065v1_genomic.fna/markers.fasta
[2024-01-24 11:59:08,708] [INFO] Task started: Blastn
[2024-01-24 11:59:08,708] [INFO] Running command: blastn -query GCF_005280655.1_ASM528065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference/reference_markers.fasta -out GCF_005280655.1_ASM528065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:09,340] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:09,346] [INFO] Selected 8 target genomes.
[2024-01-24 11:59:09,347] [INFO] Target genome list was writen to GCF_005280655.1_ASM528065v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:09,350] [INFO] Task started: fastANI
[2024-01-24 11:59:09,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cd2b89c-5c78-47e6-a817-48c9d9ece60d/GCF_005280655.1_ASM528065v1_genomic.fna.gz --refList GCF_005280655.1_ASM528065v1_genomic.fna/target_genomes.txt --output GCF_005280655.1_ASM528065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:16,240] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:16,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:16,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:16,248] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:16,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:16,248] [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
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	100.0	1195	1196	95	conclusive
Anaerostipes hominis	strain=BG01	GCA_002270485.1	2025494	2025494	type	True	84.1966	658	1196	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	82.792	733	1196	95	below_threshold
Anaerostipes caccae	strain=JCM 13470	GCA_014467075.1	105841	105841	type	True	82.751	741	1196	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_000154305.1	105841	105841	type	True	82.7364	737	1196	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_014131675.1	105841	105841	type	True	82.6873	746	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:16,250] [INFO] DFAST Taxonomy check result was written to GCF_005280655.1_ASM528065v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:16,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:16,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:16,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference/checkm_data
[2024-01-24 11:59:16,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:16,289] [INFO] Task started: CheckM
[2024-01-24 11:59:16,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005280655.1_ASM528065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005280655.1_ASM528065v1_genomic.fna/checkm_input GCF_005280655.1_ASM528065v1_genomic.fna/checkm_result
[2024-01-24 11:59:49,681] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:49,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:49,701] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:49,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:49,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005280655.1_ASM528065v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:49,702] [INFO] Task started: Blastn
[2024-01-24 11:59:49,702] [INFO] Running command: blastn -query GCF_005280655.1_ASM528065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg528ac901-1941-4c54-8d72-2627a4967b9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005280655.1_ASM528065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:50,860] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:50,864] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:50,865] [INFO] Target genome list was writen to GCF_005280655.1_ASM528065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:50,889] [INFO] Task started: fastANI
[2024-01-24 11:59:50,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cd2b89c-5c78-47e6-a817-48c9d9ece60d/GCF_005280655.1_ASM528065v1_genomic.fna.gz --refList GCF_005280655.1_ASM528065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005280655.1_ASM528065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:57,946] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:57,954] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:57,954] [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_005280655.1	s__Anaerostipes rhamnosivorans	100.0	1196	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.93	99.92	0.96	0.94	3	conclusive
GCA_018381315.1	s__Anaerostipes sp018381315	84.7581	830	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000508985.1	s__Anaerostipes sp000508985	84.1357	675	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.99	98.66	0.91	0.87	11	-
GCF_014467075.1	s__Anaerostipes caccae	82.7223	743	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.81	98.30	0.93	0.89	11	-
GCF_016586355.1	s__Anaerostipes butyraticus	77.9737	154	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.19	99.02	0.93	0.93	4	-
GCA_902362875.1	s__Anaerostipes sp900066705	77.878	103	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.31	0.96	0.92	3	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	76.7105	55	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:57,956] [INFO] GTDB search result was written to GCF_005280655.1_ASM528065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:57,956] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:57,959] [INFO] DFAST_QC result json was written to GCF_005280655.1_ASM528065v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:57,959] [INFO] DFAST_QC completed!
[2024-01-24 11:59:57,959] [INFO] Total running time: 0h1m1s