[2023-06-29 00:37:33,109] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:33,112] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:33,112] [INFO] DQC Reference Directory: /var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference
[2023-06-29 00:37:34,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:34,459] [INFO] Task started: Prodigal
[2023-06-29 00:37:34,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg48e27c3a-eb6a-43a3-a34d-d97ad11d8afc/GCA_944384635.1_E08_bin220_genomic.fna.gz | prodigal -d GCA_944384635.1_E08_bin220_genomic.fna/cds.fna -a GCA_944384635.1_E08_bin220_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:40,672] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:40,673] [INFO] Task started: HMMsearch
[2023-06-29 00:37:40,673] [INFO] Running command: hmmsearch --tblout GCA_944384635.1_E08_bin220_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference/reference_markers.hmm GCA_944384635.1_E08_bin220_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:40,895] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:40,897] [INFO] Found 6/6 markers.
[2023-06-29 00:37:40,922] [INFO] Query marker FASTA was written to GCA_944384635.1_E08_bin220_genomic.fna/markers.fasta
[2023-06-29 00:37:40,922] [INFO] Task started: Blastn
[2023-06-29 00:37:40,923] [INFO] Running command: blastn -query GCA_944384635.1_E08_bin220_genomic.fna/markers.fasta -db /var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference/reference_markers.fasta -out GCA_944384635.1_E08_bin220_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:41,648] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:41,653] [INFO] Selected 20 target genomes.
[2023-06-29 00:37:41,653] [INFO] Target genome list was writen to GCA_944384635.1_E08_bin220_genomic.fna/target_genomes.txt
[2023-06-29 00:37:41,659] [INFO] Task started: fastANI
[2023-06-29 00:37:41,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e27c3a-eb6a-43a3-a34d-d97ad11d8afc/GCA_944384635.1_E08_bin220_genomic.fna.gz --refList GCA_944384635.1_E08_bin220_genomic.fna/target_genomes.txt --output GCA_944384635.1_E08_bin220_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:54,756] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:54,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:54,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:54,770] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:54,770] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:37:54,770] [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
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	83.3437	520	713	95	below_threshold
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	79.2784	278	713	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	78.2223	187	713	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	77.7579	150	713	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	77.3147	115	713	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	77.2658	129	713	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	76.303	62	713	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	75.0281	54	713	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.872	61	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:37:54,773] [INFO] DFAST Taxonomy check result was written to GCA_944384635.1_E08_bin220_genomic.fna/tc_result.tsv
[2023-06-29 00:37:54,773] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:54,773] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:54,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference/checkm_data
[2023-06-29 00:37:54,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:54,800] [INFO] Task started: CheckM
[2023-06-29 00:37:54,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384635.1_E08_bin220_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384635.1_E08_bin220_genomic.fna/checkm_input GCA_944384635.1_E08_bin220_genomic.fna/checkm_result
[2023-06-29 00:38:18,851] [INFO] Task succeeded: CheckM
[2023-06-29 00:38:18,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:38:18,874] [INFO] ===== Completeness check finished =====
[2023-06-29 00:38:18,874] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:38:18,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384635.1_E08_bin220_genomic.fna/markers.fasta)
[2023-06-29 00:38:18,875] [INFO] Task started: Blastn
[2023-06-29 00:38:18,875] [INFO] Running command: blastn -query GCA_944384635.1_E08_bin220_genomic.fna/markers.fasta -db /var/lib/cwl/stgce77df70-926a-4f35-a881-a8e145c48c39/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384635.1_E08_bin220_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:20,218] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:20,223] [INFO] Selected 12 target genomes.
[2023-06-29 00:38:20,223] [INFO] Target genome list was writen to GCA_944384635.1_E08_bin220_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:20,231] [INFO] Task started: fastANI
[2023-06-29 00:38:20,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e27c3a-eb6a-43a3-a34d-d97ad11d8afc/GCA_944384635.1_E08_bin220_genomic.fna.gz --refList GCA_944384635.1_E08_bin220_genomic.fna/target_genomes_gtdb.txt --output GCA_944384635.1_E08_bin220_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:25,532] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:25,550] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:25,550] [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_019112985.1	s__Butyricicoccus_A stercorigallinarum	99.3326	601	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002157465.1	s__Butyricicoccus_A porcorum	83.3205	522	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.36	99.36	0.89	0.89	2	-
GCA_002449635.1	s__Butyricicoccus_A sp002449635	80.9378	297	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.64	99.40	0.85	0.80	8	-
GCF_018918345.1	s__Butyricicoccus_A sp002395695	79.2784	278	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	98.08	98.03	0.91	0.78	6	-
GCA_016293155.1	s__JAEDEU01 sp016293155	79.0987	214	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__JAEDEU01	95.0	98.88	98.88	0.85	0.85	2	-
GCA_004555915.1	s__Butyricicoccus_A sp004555915	78.793	267	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.18	99.18	0.98	0.98	2	-
GCA_900555465.1	s__Agathobaculum intestinigallinarum	78.7246	142	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCA_019114345.1	s__Agathobaculum pullistercoris	78.5622	162	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCF_900625105.1	s__Agathobaculum sp900625105	78.2184	200	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557315.1	s__Agathobaculum sp900557315	78.0877	121	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCF_003481705.1	s__Agathobaculum sp003481705	78.0568	182	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	-
GCA_000432375.1	s__CAG-103 sp000432375	76.3945	85	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:25,552] [INFO] GTDB search result was written to GCA_944384635.1_E08_bin220_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:25,553] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:25,556] [INFO] DFAST_QC result json was written to GCA_944384635.1_E08_bin220_genomic.fna/dqc_result.json
[2023-06-29 00:38:25,557] [INFO] DFAST_QC completed!
[2023-06-29 00:38:25,557] [INFO] Total running time: 0h0m52s