[2023-06-08 05:33:52,085] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:33:52,094] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:33:52,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference
[2023-06-08 05:33:53,433] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:33:53,434] [INFO] Task started: Prodigal
[2023-06-08 05:33:53,434] [INFO] Running command: gunzip -c /var/lib/cwl/stgf40e7e09-4801-47a4-9bba-90a16dcd5bb4/GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:34:14,169] [INFO] Task succeeded: Prodigal
[2023-06-08 05:34:14,170] [INFO] Task started: HMMsearch
[2023-06-08 05:34:14,170] [INFO] Running command: hmmsearch --tblout GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference/reference_markers.hmm GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:34:14,443] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:34:14,445] [INFO] Found 6/6 markers.
[2023-06-08 05:34:14,482] [INFO] Query marker FASTA was written to GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:34:14,483] [INFO] Task started: Blastn
[2023-06-08 05:34:14,483] [INFO] Running command: blastn -query GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference/reference_markers.fasta -out GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:34:15,088] [INFO] Task succeeded: Blastn
[2023-06-08 05:34:15,092] [INFO] Selected 10 target genomes.
[2023-06-08 05:34:15,092] [INFO] Target genome list was writen to GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:34:15,093] [INFO] Task started: fastANI
[2023-06-08 05:34:15,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgf40e7e09-4801-47a4-9bba-90a16dcd5bb4/GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:34:24,105] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:24,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:34:24,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:34:24,123] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:34:24,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:34:24,124] [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
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	93.0715	900	1275	95	below_threshold
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	92.9976	879	1275	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	90.4779	846	1275	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	90.4256	850	1275	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_000156075.1	357276	357276	type	True	89.8971	849	1275	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	89.8427	843	1275	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	89.8168	858	1275	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	81.0252	508	1275	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.5857	145	1275	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	77.4026	147	1275	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:34:24,126] [INFO] DFAST Taxonomy check result was written to GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:34:24,127] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:34:24,127] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:34:24,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference/checkm_data
[2023-06-08 05:34:24,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:34:24,175] [INFO] Task started: CheckM
[2023-06-08 05:34:24,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:35:22,782] [INFO] Task succeeded: CheckM
[2023-06-08 05:35:22,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:35:22,802] [INFO] ===== Completeness check finished =====
[2023-06-08 05:35:22,802] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:35:22,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:35:22,803] [INFO] Task started: Blastn
[2023-06-08 05:35:22,803] [INFO] Running command: blastn -query GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b642006-ae77-42cf-bd1c-2fcc5c43e2c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:35:23,629] [INFO] Task succeeded: Blastn
[2023-06-08 05:35:23,634] [INFO] Selected 6 target genomes.
[2023-06-08 05:35:23,634] [INFO] Target genome list was writen to GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:35:23,635] [INFO] Task started: fastANI
[2023-06-08 05:35:23,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgf40e7e09-4801-47a4-9bba-90a16dcd5bb4/GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:35:29,755] [INFO] Task succeeded: fastANI
[2023-06-08 05:35:29,766] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:35:29,766] [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_011959205.1	s__Phocaeicola sp011959205	99.8424	1122	1275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	conclusive
GCF_000614185.1	s__Phocaeicola sartorii	93.0137	878	1275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCF_000012825.1	s__Phocaeicola vulgatus	90.4418	849	1275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	-
GCF_013009555.1	s__Phocaeicola dorei	89.8275	857	1275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	-
GCA_900760795.1	s__Phocaeicola sp900760795	86.4578	608	1275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388365.1	s__Phocaeicola sp902388365	81.2402	657	1275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-08 05:35:29,768] [INFO] GTDB search result was written to GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:35:29,769] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:35:29,772] [INFO] DFAST_QC result json was written to GCA_947072895.1_SRR12464007_bin.12_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:35:29,772] [INFO] DFAST_QC completed!
[2023-06-08 05:35:29,772] [INFO] Total running time: 0h1m38s