[2023-06-08 00:34:52,633] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:34:52,635] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:34:52,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference
[2023-06-08 00:34:53,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:34:53,895] [INFO] Task started: Prodigal
[2023-06-08 00:34:53,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg90f9cbfc-c9da-4e52-9adc-387aab5b8461/GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:00,595] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:00,595] [INFO] Task started: HMMsearch
[2023-06-08 00:35:00,596] [INFO] Running command: hmmsearch --tblout GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference/reference_markers.hmm GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:00,822] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:00,823] [INFO] Found 6/6 markers.
[2023-06-08 00:35:00,851] [INFO] Query marker FASTA was written to GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:35:00,851] [INFO] Task started: Blastn
[2023-06-08 00:35:00,851] [INFO] Running command: blastn -query GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference/reference_markers.fasta -out GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:01,408] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:01,412] [INFO] Selected 21 target genomes.
[2023-06-08 00:35:01,413] [INFO] Target genome list was writen to GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:35:01,414] [INFO] Task started: fastANI
[2023-06-08 00:35:01,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg90f9cbfc-c9da-4e52-9adc-387aab5b8461/GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:12,859] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:12,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:12,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:12,870] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:12,870] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:35:12,870] [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
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	78.8848	351	1013	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	77.6209	185	1013	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.5964	186	1013	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.3663	149	1013	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.2664	131	1013	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	77.253	125	1013	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.2321	123	1013	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	76.7982	130	1013	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.7702	130	1013	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.3551	69	1013	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:35:12,872] [INFO] DFAST Taxonomy check result was written to GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:35:12,873] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:12,873] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:12,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference/checkm_data
[2023-06-08 00:35:12,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:12,905] [INFO] Task started: CheckM
[2023-06-08 00:35:12,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:35:38,154] [INFO] Task succeeded: CheckM
[2023-06-08 00:35:38,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:35:38,171] [INFO] ===== Completeness check finished =====
[2023-06-08 00:35:38,172] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:35:38,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:35:38,173] [INFO] Task started: Blastn
[2023-06-08 00:35:38,173] [INFO] Running command: blastn -query GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c67804d-b5e1-4178-be8a-29b7a620f6cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:38,998] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:39,002] [INFO] Selected 11 target genomes.
[2023-06-08 00:35:39,002] [INFO] Target genome list was writen to GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:35:39,004] [INFO] Task started: fastANI
[2023-06-08 00:35:39,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg90f9cbfc-c9da-4e52-9adc-387aab5b8461/GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:35:48,730] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:48,740] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:35:48,740] [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_910585725.1	s__Sporofaciens sp910585725	99.704	954	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910574285.1	s__Sporofaciens sp009774295	89.7411	804	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.51	98.02	0.91	0.84	4	-
GCF_000403455.2	s__Sporofaciens sp000403455	81.0967	586	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.91	98.91	0.91	0.91	2	-
GCA_910579015.1	s__Sporofaciens sp910579015	79.6773	411	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574715.1	s__Sporofaciens sp910574715	79.6046	437	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.89	98.89	0.95	0.95	2	-
GCA_910575835.1	s__Sporofaciens sp910575835	79.3599	441	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577685.1	s__Sporofaciens sp910577685	79.1984	370	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574885.1	s__Sporofaciens sp910574885	78.9201	356	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	99.41	98.81	0.91	0.83	5	-
GCF_009830285.1	s__Sporofaciens musculi	78.8787	352	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	97.72	97.71	0.87	0.86	3	-
GCF_900240315.1	s__Dorea_B phocaeensis	77.2664	131	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCA_900549995.1	s__UMGS1251 sp900549995	75.748	66	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1251	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:35:48,742] [INFO] GTDB search result was written to GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:35:48,742] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:35:48,745] [INFO] DFAST_QC result json was written to GCA_947573685.1_SRR15730554_bin.62_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:35:48,745] [INFO] DFAST_QC completed!
[2023-06-08 00:35:48,745] [INFO] Total running time: 0h0m56s