[2023-06-16 19:17:28,866] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:17:28,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:17:28,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference
[2023-06-16 19:17:29,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:17:29,976] [INFO] Task started: Prodigal
[2023-06-16 19:17:29,976] [INFO] Running command: gunzip -c /var/lib/cwl/stgea5e513d-010c-4364-9700-be1e5344fb25/GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna.gz | prodigal -d GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/cds.fna -a GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:17:34,481] [INFO] Task succeeded: Prodigal
[2023-06-16 19:17:34,481] [INFO] Task started: HMMsearch
[2023-06-16 19:17:34,481] [INFO] Running command: hmmsearch --tblout GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference/reference_markers.hmm GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:17:34,673] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:17:34,674] [INFO] Found 6/6 markers.
[2023-06-16 19:17:34,699] [INFO] Query marker FASTA was written to GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/markers.fasta
[2023-06-16 19:17:34,699] [INFO] Task started: Blastn
[2023-06-16 19:17:34,699] [INFO] Running command: blastn -query GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference/reference_markers.fasta -out GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:17:35,331] [INFO] Task succeeded: Blastn
[2023-06-16 19:17:35,334] [INFO] Selected 25 target genomes.
[2023-06-16 19:17:35,334] [INFO] Target genome list was writen to GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/target_genomes.txt
[2023-06-16 19:17:35,337] [INFO] Task started: fastANI
[2023-06-16 19:17:35,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgea5e513d-010c-4364-9700-be1e5344fb25/GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna.gz --refList GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/target_genomes.txt --output GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:17:48,454] [INFO] Task succeeded: fastANI
[2023-06-16 19:17:48,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:17:48,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:17:48,460] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:17:48,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:17:48,460] [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
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	77.5048	74	564	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.471	55	564	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.6738	53	564	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.578	57	564	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.2943	52	564	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:17:48,461] [INFO] DFAST Taxonomy check result was written to GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/tc_result.tsv
[2023-06-16 19:17:48,462] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:17:48,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:17:48,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference/checkm_data
[2023-06-16 19:17:48,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:17:48,484] [INFO] Task started: CheckM
[2023-06-16 19:17:48,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/checkm_input GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/checkm_result
[2023-06-16 19:18:06,450] [INFO] Task succeeded: CheckM
[2023-06-16 19:18:06,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:18:06,479] [INFO] ===== Completeness check finished =====
[2023-06-16 19:18:06,479] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:18:06,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/markers.fasta)
[2023-06-16 19:18:06,480] [INFO] Task started: Blastn
[2023-06-16 19:18:06,480] [INFO] Running command: blastn -query GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d4b416-f52a-4948-91b2-2be6b9d2ea22/dqc_reference/reference_markers_gtdb.fasta -out GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:18:07,630] [INFO] Task succeeded: Blastn
[2023-06-16 19:18:07,634] [INFO] Selected 10 target genomes.
[2023-06-16 19:18:07,634] [INFO] Target genome list was writen to GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:18:07,663] [INFO] Task started: fastANI
[2023-06-16 19:18:07,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgea5e513d-010c-4364-9700-be1e5344fb25/GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna.gz --refList GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/target_genomes_gtdb.txt --output GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:18:11,463] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:11,469] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:18:11,469] [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_900547385.1	s__Angelakisella sp900547385	98.1796	507	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	97.71	97.52	0.88	0.82	7	conclusive
GCA_003453215.1	s__Angelakisella sp003453215	85.8636	334	564	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_004557855.1	s__Angelakisella sp004557855	85.7801	421	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	98.10	97.70	0.90	0.86	7	-
GCA_900552845.1	s__Angelakisella sp900552845	84.2088	323	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	98.71	98.15	0.74	0.74	3	-
GCA_004554485.1	s__Angelakisella sp004554485	82.4924	307	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	97.18	96.00	0.84	0.76	6	-
--------------------------------------------------------------------------------
[2023-06-16 19:18:11,471] [INFO] GTDB search result was written to GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/result_gtdb.tsv
[2023-06-16 19:18:11,471] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:18:11,474] [INFO] DFAST_QC result json was written to GCA_905197705.1_ERR1190883-mag-bin.73_genomic.fna/dqc_result.json
[2023-06-16 19:18:11,474] [INFO] DFAST_QC completed!
[2023-06-16 19:18:11,474] [INFO] Total running time: 0h0m43s