[2023-06-08 13:33:26,827] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:33:26,832] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:33:26,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference
[2023-06-08 13:33:27,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:33:27,947] [INFO] Task started: Prodigal
[2023-06-08 13:33:27,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg977f2586-15a3-43d6-88ef-a4a70764d3cf/GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:33:36,436] [INFO] Task succeeded: Prodigal
[2023-06-08 13:33:36,436] [INFO] Task started: HMMsearch
[2023-06-08 13:33:36,436] [INFO] Running command: hmmsearch --tblout GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference/reference_markers.hmm GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:33:36,657] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:33:36,658] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg977f2586-15a3-43d6-88ef-a4a70764d3cf/GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 13:33:36,688] [INFO] Query marker FASTA was written to GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:33:36,689] [INFO] Task started: Blastn
[2023-06-08 13:33:36,689] [INFO] Running command: blastn -query GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference/reference_markers.fasta -out GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:37,255] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:37,258] [INFO] Selected 19 target genomes.
[2023-06-08 13:33:37,258] [INFO] Target genome list was writen to GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:33:37,259] [INFO] Task started: fastANI
[2023-06-08 13:33:37,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg977f2586-15a3-43d6-88ef-a4a70764d3cf/GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:33:46,907] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:46,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:33:46,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:33:46,917] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:33:46,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:33:46,918] [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
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	79.3231	514	1261	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	77.2406	88	1261	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.2085	140	1261	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.1227	144	1261	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.1053	146	1261	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.1017	139	1261	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.0918	142	1261	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	77.0669	145	1261	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.0432	76	1261	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	76.9159	111	1261	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.8923	116	1261	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	76.8406	74	1261	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.7485	72	1261	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	76.3933	77	1261	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	76.3733	75	1261	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.2494	50	1261	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:33:46,924] [INFO] DFAST Taxonomy check result was written to GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:33:46,925] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:33:46,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:33:46,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference/checkm_data
[2023-06-08 13:33:46,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:33:46,966] [INFO] Task started: CheckM
[2023-06-08 13:33:46,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:34:15,123] [INFO] Task succeeded: CheckM
[2023-06-08 13:34:15,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:34:15,144] [INFO] ===== Completeness check finished =====
[2023-06-08 13:34:15,144] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:34:15,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:34:15,145] [INFO] Task started: Blastn
[2023-06-08 13:34:15,145] [INFO] Running command: blastn -query GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a9812c6-d9a4-4551-9d0d-360940398c9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:34:16,035] [INFO] Task succeeded: Blastn
[2023-06-08 13:34:16,037] [INFO] Selected 10 target genomes.
[2023-06-08 13:34:16,038] [INFO] Target genome list was writen to GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:34:16,043] [INFO] Task started: fastANI
[2023-06-08 13:34:16,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg977f2586-15a3-43d6-88ef-a4a70764d3cf/GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:34:24,699] [INFO] Task succeeded: fastANI
[2023-06-08 13:34:24,708] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:34:24,708] [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_910589385.1	s__Schaedlerella sp910589385	99.6364	1109	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910575475.1	s__Schaedlerella sp910575475	80.3922	538	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.35	99.35	0.93	0.93	2	-
GCA_009911175.1	s__Schaedlerella sp009911175	80.1566	547	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCA_000403295.2	s__Schaedlerella sp000403295	79.7262	521	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
GCA_009774255.1	s__Schaedlerella sp009774255	79.5175	518	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003885045.1	s__Schaedlerella arabinosiphila	79.3599	510	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.52	96.80	0.74	0.68	10	-
GCA_910574195.1	s__Schaedlerella sp910574195	77.8532	254	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_004556565.1	s__Schaedlerella sp004556565	77.5199	130	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320245.1	s__Schaedlerella sp002320245	77.3494	139	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119205.1	s__Mediterraneibacter intestinavium	76.9927	98	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.10	98.10	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-08 13:34:24,713] [INFO] GTDB search result was written to GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:34:24,714] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:34:24,717] [INFO] DFAST_QC result json was written to GCA_947574415.1_SRR15730548_bin.12_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:34:24,717] [INFO] DFAST_QC completed!
[2023-06-08 13:34:24,717] [INFO] Total running time: 0h0m58s