[2023-06-13 09:11:57,817] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:11:57,824] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:11:57,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference
[2023-06-13 09:11:59,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:11:59,358] [INFO] Task started: Prodigal
[2023-06-13 09:11:59,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg841ff55e-f30a-44ad-b81a-147c5416510f/GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:11,699] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:11,699] [INFO] Task started: HMMsearch
[2023-06-13 09:12:11,699] [INFO] Running command: hmmsearch --tblout GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference/reference_markers.hmm GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:11,967] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:11,968] [INFO] Found 6/6 markers.
[2023-06-13 09:12:11,996] [INFO] Query marker FASTA was written to GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 09:12:11,996] [INFO] Task started: Blastn
[2023-06-13 09:12:11,996] [INFO] Running command: blastn -query GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference/reference_markers.fasta -out GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:12,662] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:12,666] [INFO] Selected 27 target genomes.
[2023-06-13 09:12:12,667] [INFO] Target genome list was writen to GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 09:12:12,672] [INFO] Task started: fastANI
[2023-06-13 09:12:12,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg841ff55e-f30a-44ad-b81a-147c5416510f/GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:33,556] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:33,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:33,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:33,564] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:33,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:12:33,565] [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
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	76.9494	53	646	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.8587	85	646	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.8434	68	646	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.7264	67	646	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.6288	63	646	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:12:33,570] [INFO] DFAST Taxonomy check result was written to GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 09:12:33,570] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:33,571] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:33,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference/checkm_data
[2023-06-13 09:12:33,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:33,599] [INFO] Task started: CheckM
[2023-06-13 09:12:33,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 09:13:12,841] [INFO] Task succeeded: CheckM
[2023-06-13 09:13:12,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:13:12,869] [INFO] ===== Completeness check finished =====
[2023-06-13 09:13:12,870] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:13:12,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 09:13:12,871] [INFO] Task started: Blastn
[2023-06-13 09:13:12,871] [INFO] Running command: blastn -query GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg480b05eb-c6f5-4c0f-8db5-ed6d9919c1ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:13:13,710] [INFO] Task succeeded: Blastn
[2023-06-13 09:13:13,716] [INFO] Selected 22 target genomes.
[2023-06-13 09:13:13,716] [INFO] Target genome list was writen to GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:13:13,725] [INFO] Task started: fastANI
[2023-06-13 09:13:13,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg841ff55e-f30a-44ad-b81a-147c5416510f/GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:13:22,202] [INFO] Task succeeded: fastANI
[2023-06-13 09:13:22,223] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:13:22,223] [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_011959405.1	s__UBA3263 sp001689615	99.2025	460	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	99.21	99.09	0.70	0.66	12	conclusive
GCA_002490725.1	s__UBA3263 sp002490725	77.9844	100	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	99.93	99.92	0.89	0.85	3	-
GCA_900759865.1	s__UBA3263 sp900759865	77.6131	103	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802435.1	s__UBA3263 sp014802435	77.4482	67	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	97.99	97.67	0.88	0.83	9	-
GCA_001689495.1	s__Duncaniella sp001689495	77.4255	76	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.23	99.23	0.93	0.93	2	-
GCA_014801955.1	s__UBA3263 sp014801955	77.2892	81	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	97.82	97.69	0.84	0.82	6	-
GCA_014801075.1	s__UBA7173 sp014801075	77.045	75	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.74	97.55	0.90	0.88	4	-
GCA_001701225.1	s__Duncaniella sp001701225	77.0106	59	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.71	98.22	0.91	0.86	3	-
GCA_900762315.1	s__Duncaniella sp900762315	76.9222	68	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586565.1	s__UBA7173 sp910586565	76.8758	78	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024805.1	s__Duncaniella muris	76.8587	85	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	-
GCA_009775265.1	s__CAG-873 sp009775265	76.8324	75	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.34	99.23	0.92	0.92	3	-
GCA_910586975.1	s__CAG-873 sp910586975	76.7423	56	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803695.1	s__Muribaculum gordoncarteri	76.6288	63	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCA_900759915.1	s__Paramuribaculum sp900759915	76.4311	69	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_014802015.1	s__Duncaniella sp014802015	76.3941	67	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800605.1	s__UBA7173 sp014800605	76.3539	57	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:13:22,225] [INFO] GTDB search result was written to GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 09:13:22,226] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:13:22,242] [INFO] DFAST_QC result json was written to GCA_947577215.1_SRR15730536_bin.29_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 09:13:22,242] [INFO] DFAST_QC completed!
[2023-06-13 09:13:22,242] [INFO] Total running time: 0h1m24s