[2023-06-29 03:47:03,334] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:47:03,337] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:47:03,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference
[2023-06-29 03:47:04,602] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:47:04,603] [INFO] Task started: Prodigal
[2023-06-29 03:47:04,604] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1a3f970-fa96-4ae0-9d5b-4c8cbcd244ad/GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:47:20,506] [INFO] Task succeeded: Prodigal
[2023-06-29 03:47:20,507] [INFO] Task started: HMMsearch
[2023-06-29 03:47:20,507] [INFO] Running command: hmmsearch --tblout GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference/reference_markers.hmm GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:47:20,762] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:47:20,763] [INFO] Found 6/6 markers.
[2023-06-29 03:47:20,791] [INFO] Query marker FASTA was written to GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 03:47:20,791] [INFO] Task started: Blastn
[2023-06-29 03:47:20,792] [INFO] Running command: blastn -query GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference/reference_markers.fasta -out GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:21,454] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:21,459] [INFO] Selected 20 target genomes.
[2023-06-29 03:47:21,459] [INFO] Target genome list was writen to GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 03:47:21,463] [INFO] Task started: fastANI
[2023-06-29 03:47:21,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1a3f970-fa96-4ae0-9d5b-4c8cbcd244ad/GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:47:35,195] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:35,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:47:35,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:47:35,207] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:47:35,207] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:47:35,207] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	78.3191	67	873	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.8452	81	873	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	77.2763	72	873	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.1666	69	873	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.165	73	873	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.1638	74	873	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.149	64	873	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:47:35,210] [INFO] DFAST Taxonomy check result was written to GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 03:47:35,210] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:47:35,211] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:47:35,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference/checkm_data
[2023-06-29 03:47:35,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:47:35,253] [INFO] Task started: CheckM
[2023-06-29 03:47:35,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 03:48:22,904] [INFO] Task succeeded: CheckM
[2023-06-29 03:48:22,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:48:22,930] [INFO] ===== Completeness check finished =====
[2023-06-29 03:48:22,930] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:48:22,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 03:48:22,931] [INFO] Task started: Blastn
[2023-06-29 03:48:22,931] [INFO] Running command: blastn -query GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg392a8e5f-d3ed-4bd3-960f-1ea3d2dcf51f/dqc_reference/reference_markers_gtdb.fasta -out GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:48:23,789] [INFO] Task succeeded: Blastn
[2023-06-29 03:48:23,794] [INFO] Selected 20 target genomes.
[2023-06-29 03:48:23,794] [INFO] Target genome list was writen to GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:48:23,802] [INFO] Task started: fastANI
[2023-06-29 03:48:23,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1a3f970-fa96-4ae0-9d5b-4c8cbcd244ad/GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:48:33,013] [INFO] Task succeeded: fastANI
[2023-06-29 03:48:33,041] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 03:48:33,041] [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_910575545.1	s__UBA7173 sp013316675	99.3839	820	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.44	98.97	0.94	0.91	3	conclusive
GCA_001689485.1	s__UBA7173 sp001689485	78.5001	221	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.04	99.00	0.86	0.84	5	-
GCA_013316535.1	s__UBA7173 sp013316535	78.425	147	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.52	97.52	0.95	0.95	2	-
GCA_910575615.1	s__UBA7173 sp001689685	78.1447	153	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.70	99.58	0.97	0.94	9	-
GCA_910586565.1	s__UBA7173 sp910586565	78.1185	222	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540205.1	s__UBA7173 sp900540205	77.7505	170	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.71	95.96	0.83	0.74	4	-
GCA_004102785.1	s__UBA7173 sp002491305	77.728	138	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.18	98.68	0.94	0.92	6	-
GCA_900545955.1	s__UBA7173 sp900545955	77.6974	129	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.61	97.55	0.88	0.85	4	-
GCA_001701135.1	s__UBA7173 sp001701135	77.5698	114	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.33	96.66	0.85	0.83	3	-
GCA_910583675.1	s__UBA7173 sp910583675	77.5572	139	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546835.1	s__UBA7173 sp900546835	77.4808	121	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.67	99.65	0.91	0.86	3	-
GCA_004557825.1	s__UBA7173 sp004557825	77.2835	91	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584735.1	s__UBA7173 sp910584735	77.2152	115	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578035.1	s__CAG-873 sp910578035	76.8504	69	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587075.1	s__UBA7173 sp910587075	76.7583	115	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577255.1	s__Duncaniella sp910577255	76.4641	69	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586665.1	s__Duncaniella sp910586665	76.4527	77	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579105.1	s__UBA7173 sp910579105	76.424	97	873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:48:33,043] [INFO] GTDB search result was written to GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 03:48:33,044] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:48:33,047] [INFO] DFAST_QC result json was written to GCA_948435045.1_SRR18243796_bin.20_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 03:48:33,047] [INFO] DFAST_QC completed!
[2023-06-29 03:48:33,048] [INFO] Total running time: 0h1m30s