[2023-06-14 00:42:47,517] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:42:47,519] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:42:47,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference
[2023-06-14 00:42:48,751] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:42:48,752] [INFO] Task started: Prodigal
[2023-06-14 00:42:48,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg67f378fa-3556-4a80-9699-e19924ea379e/GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:42:55,030] [INFO] Task succeeded: Prodigal
[2023-06-14 00:42:55,031] [INFO] Task started: HMMsearch
[2023-06-14 00:42:55,031] [INFO] Running command: hmmsearch --tblout GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference/reference_markers.hmm GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:42:55,271] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:42:55,273] [INFO] Found 6/6 markers.
[2023-06-14 00:42:55,298] [INFO] Query marker FASTA was written to GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-14 00:42:55,299] [INFO] Task started: Blastn
[2023-06-14 00:42:55,299] [INFO] Running command: blastn -query GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference/reference_markers.fasta -out GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:42:55,912] [INFO] Task succeeded: Blastn
[2023-06-14 00:42:55,917] [INFO] Selected 16 target genomes.
[2023-06-14 00:42:55,918] [INFO] Target genome list was writen to GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-14 00:42:55,920] [INFO] Task started: fastANI
[2023-06-14 00:42:55,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg67f378fa-3556-4a80-9699-e19924ea379e/GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:43:02,710] [INFO] Task succeeded: fastANI
[2023-06-14 00:43:02,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:43:02,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:43:02,727] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:43:02,727] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 00:43:02,727] [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
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	91.0788	571	666	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	80.7086	310	666	95	below_threshold
Slackia equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	78.3591	182	666	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_003725955.1	572010	572010	type	True	78.292	152	666	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_014192995.1	572010	572010	type	True	78.2517	146	666	95	below_threshold
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	78.0938	123	666	95	below_threshold
Slackia heliotrinireducens	strain=NCTC11029	GCA_900637575.1	84110	84110	type	True	77.6858	111	666	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	77.6818	122	666	95	below_threshold
Slackia exigua	strain=ATCC 700122	GCA_000162875.1	84109	84109	type	True	77.6724	104	666	95	below_threshold
Slackia heliotrinireducens	strain=DSM 20476	GCA_000023885.1	84110	84110	type	True	77.6365	112	666	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	77.5521	52	666	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	77.3493	130	666	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	77.3261	142	666	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_017945865.1	2682776	2682776	type	True	77.1215	83	666	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_011392455.1	2682776	2682776	type	True	77.0223	88	666	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:43:02,729] [INFO] DFAST Taxonomy check result was written to GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-14 00:43:02,730] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:43:02,730] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:43:02,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference/checkm_data
[2023-06-14 00:43:02,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:43:02,755] [INFO] Task started: CheckM
[2023-06-14 00:43:02,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-14 00:43:27,330] [INFO] Task succeeded: CheckM
[2023-06-14 00:43:27,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.26%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:43:27,355] [INFO] ===== Completeness check finished =====
[2023-06-14 00:43:27,355] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:43:27,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-14 00:43:27,356] [INFO] Task started: Blastn
[2023-06-14 00:43:27,356] [INFO] Running command: blastn -query GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcab59a5b-10e8-4f56-98f9-95287d0fa371/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:43:28,248] [INFO] Task succeeded: Blastn
[2023-06-14 00:43:28,253] [INFO] Selected 12 target genomes.
[2023-06-14 00:43:28,253] [INFO] Target genome list was writen to GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:43:28,257] [INFO] Task started: fastANI
[2023-06-14 00:43:28,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg67f378fa-3556-4a80-9699-e19924ea379e/GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:43:33,121] [INFO] Task succeeded: fastANI
[2023-06-14 00:43:33,135] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:43:33,135] [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_900553655.1	s__Slackia_A sp900553655	98.2695	332	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	97.68	97.68	0.69	0.69	2	conclusive
GCF_000296445.1	s__Slackia_A piriformis	91.0788	571	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.02	96.04	0.96	0.92	3	-
GCF_003725295.1	s__Slackia_A faecicanis	80.7287	309	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553775.1	s__Slackia_A sp900553775	80.3094	239	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.24	98.24	0.77	0.77	2	-
GCA_900555495.1	s__Slackia_A sp900555495	79.7404	194	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	100.00	100.00	0.96	0.96	2	-
GCF_003725995.1	s__Slackia_A equolifaciens	78.3591	182	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725955.1	s__Slackia_A isoflavoniconvertens	78.3156	151	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	96.92	96.02	0.86	0.81	13	-
GCF_000023885.1	s__Slackia heliotrinireducens	77.6178	112	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004135645.1	s__Senegalimassilia faecalis	77.6056	113	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.85	96.73	0.92	0.89	4	-
GCF_008831035.1	s__Ellagibacter isourolithinifaciens	77.1474	98	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	96.52	96.27	0.85	0.76	13	-
GCA_017945865.1	s__D16-34 sp011392455	77.1274	82	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-34	95.0	97.96	96.85	0.90	0.86	4	-
GCA_910585575.1	s__Adlercreutzia sp910585575	76.657	87	666	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:43:33,138] [INFO] GTDB search result was written to GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 00:43:33,138] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:43:33,144] [INFO] DFAST_QC result json was written to GCA_938005385.1_ERR912019_bin.72_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-14 00:43:33,144] [INFO] DFAST_QC completed!
[2023-06-14 00:43:33,144] [INFO] Total running time: 0h0m46s