[2024-01-24 13:36:45,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference
[2024-01-24 13:36:47,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,121] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg07218544-e9ae-473d-b99e-80ed131ef583/GCF_021109255.1_ASM2110925v1_genomic.fna.gz | prodigal -d GCF_021109255.1_ASM2110925v1_genomic.fna/cds.fna -a GCF_021109255.1_ASM2110925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:54,322] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:54,322] [INFO] Task started: HMMsearch
[2024-01-24 13:36:54,322] [INFO] Running command: hmmsearch --tblout GCF_021109255.1_ASM2110925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference/reference_markers.hmm GCF_021109255.1_ASM2110925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:54,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:54,543] [INFO] Found 6/6 markers.
[2024-01-24 13:36:54,565] [INFO] Query marker FASTA was written to GCF_021109255.1_ASM2110925v1_genomic.fna/markers.fasta
[2024-01-24 13:36:54,565] [INFO] Task started: Blastn
[2024-01-24 13:36:54,565] [INFO] Running command: blastn -query GCF_021109255.1_ASM2110925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference/reference_markers.fasta -out GCF_021109255.1_ASM2110925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:55,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:55,281] [INFO] Selected 17 target genomes.
[2024-01-24 13:36:55,281] [INFO] Target genome list was writen to GCF_021109255.1_ASM2110925v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:55,295] [INFO] Task started: fastANI
[2024-01-24 13:36:55,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg07218544-e9ae-473d-b99e-80ed131ef583/GCF_021109255.1_ASM2110925v1_genomic.fna.gz --refList GCF_021109255.1_ASM2110925v1_genomic.fna/target_genomes.txt --output GCF_021109255.1_ASM2110925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:03,775] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:03,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:03,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:03,785] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:03,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:03,786] [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
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	99.2997	706	731	95	conclusive
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	78.7896	83	731	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	77.9832	105	731	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.6852	69	731	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	77.3469	110	731	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.2837	71	731	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.282	81	731	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.2389	65	731	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.0271	73	731	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	76.9323	53	731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:03,790] [INFO] DFAST Taxonomy check result was written to GCF_021109255.1_ASM2110925v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:03,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:03,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:03,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference/checkm_data
[2024-01-24 13:37:03,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:03,817] [INFO] Task started: CheckM
[2024-01-24 13:37:03,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021109255.1_ASM2110925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021109255.1_ASM2110925v1_genomic.fna/checkm_input GCF_021109255.1_ASM2110925v1_genomic.fna/checkm_result
[2024-01-24 13:37:30,390] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:30,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:30,407] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:30,407] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:30,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021109255.1_ASM2110925v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:30,407] [INFO] Task started: Blastn
[2024-01-24 13:37:30,408] [INFO] Running command: blastn -query GCF_021109255.1_ASM2110925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b182ffd-8aad-4f06-8820-eb8489ebf48e/dqc_reference/reference_markers_gtdb.fasta -out GCF_021109255.1_ASM2110925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:31,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:31,586] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:31,586] [INFO] Target genome list was writen to GCF_021109255.1_ASM2110925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:31,645] [INFO] Task started: fastANI
[2024-01-24 13:37:31,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg07218544-e9ae-473d-b99e-80ed131ef583/GCF_021109255.1_ASM2110925v1_genomic.fna.gz --refList GCF_021109255.1_ASM2110925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021109255.1_ASM2110925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:40,719] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:40,733] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:40,734] [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_900104615.1	s__Phocea massiliensis	99.2997	706	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Phocea	95.0	99.45	98.96	0.93	0.87	5	conclusive
GCA_900761965.1	s__Avimicrobium sp900761965	78.4776	63	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	98.03	98.03	0.92	0.92	2	-
GCA_014385095.1	s__Pararuminococcus sp014385095	77.7961	118	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pararuminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904398325.1	s__Neoruminococcus faecicola	77.6962	99	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017566145.1	s__Bittarella massiliensis_A	77.6148	94	731	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_001486165.1	s__Bittarella massiliensis	77.3741	109	731	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_904387055.1	s__Heteroruminococcus faecigallinarum	77.326	116	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Heteroruminococcus	95.0	99.97	99.97	0.96	0.96	2	-
GCA_910585525.1	s__Angelakisella sp910585525	77.2216	117	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901815.1	s__Avimicrobium caecorum	77.0761	87	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	98.00	97.74	0.94	0.92	7	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	77.0349	92	731	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_904420255.1	s__Angelakisella sp904420255	76.908	94	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904397835.1	s__Aristotella avistercoris	76.8544	100	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Aristotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904420045.1	s__Metaruminococcus caecorum	76.8083	74	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Metaruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904398655.1	s__Anaerotruncus sp904398655	76.5936	60	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017408855.1	s__UBA3818 sp017408855	76.5326	54	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA3818	95.0	97.96	97.77	0.79	0.77	5	-
GCA_000435395.1	s__Acutalibacter ornithocaccae	76.491	66	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.90	97.28	0.83	0.80	5	-
GCA_910585535.1	s__Angelakisella sp910585535	76.4351	92	731	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:40,737] [INFO] GTDB search result was written to GCF_021109255.1_ASM2110925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:40,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:40,741] [INFO] DFAST_QC result json was written to GCF_021109255.1_ASM2110925v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:40,741] [INFO] DFAST_QC completed!
[2024-01-24 13:37:40,741] [INFO] Total running time: 0h0m55s