[2023-06-18 18:52:27,071] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:52:27,083] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:52:27,083] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference
[2023-06-18 18:52:29,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:52:29,392] [INFO] Task started: Prodigal
[2023-06-18 18:52:29,393] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7d1ccbb-355d-478d-95e4-05e5ac0c21f1/GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:52:36,777] [INFO] Task succeeded: Prodigal
[2023-06-18 18:52:36,777] [INFO] Task started: HMMsearch
[2023-06-18 18:52:36,778] [INFO] Running command: hmmsearch --tblout GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference/reference_markers.hmm GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:52:37,046] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:52:37,048] [INFO] Found 6/6 markers.
[2023-06-18 18:52:37,081] [INFO] Query marker FASTA was written to GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 18:52:37,081] [INFO] Task started: Blastn
[2023-06-18 18:52:37,082] [INFO] Running command: blastn -query GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference/reference_markers.fasta -out GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:52:37,652] [INFO] Task succeeded: Blastn
[2023-06-18 18:52:37,657] [INFO] Selected 32 target genomes.
[2023-06-18 18:52:37,657] [INFO] Target genome list was writen to GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 18:52:37,661] [INFO] Task started: fastANI
[2023-06-18 18:52:37,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7d1ccbb-355d-478d-95e4-05e5ac0c21f1/GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:52:57,223] [INFO] Task succeeded: fastANI
[2023-06-18 18:52:57,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:52:57,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:52:57,243] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:52:57,243] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:52:57,244] [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
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.8081	88	1037	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.7929	85	1037	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.604	95	1037	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.5801	91	1037	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.566	87	1037	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.5176	99	1037	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.5131	99	1037	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.3126	105	1037	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.3102	105	1037	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.3072	103	1037	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.2958	89	1037	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:52:57,246] [INFO] DFAST Taxonomy check result was written to GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 18:52:57,247] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:52:57,247] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:52:57,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference/checkm_data
[2023-06-18 18:52:57,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:52:57,289] [INFO] Task started: CheckM
[2023-06-18 18:52:57,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 18:53:24,860] [INFO] Task succeeded: CheckM
[2023-06-18 18:53:24,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:53:24,890] [INFO] ===== Completeness check finished =====
[2023-06-18 18:53:24,891] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:53:24,891] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 18:53:24,892] [INFO] Task started: Blastn
[2023-06-18 18:53:24,892] [INFO] Running command: blastn -query GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea8a319-c82f-400b-b024-0308987ae18a/dqc_reference/reference_markers_gtdb.fasta -out GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:53:25,659] [INFO] Task succeeded: Blastn
[2023-06-18 18:53:25,664] [INFO] Selected 20 target genomes.
[2023-06-18 18:53:25,665] [INFO] Target genome list was writen to GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:53:25,677] [INFO] Task started: fastANI
[2023-06-18 18:53:25,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7d1ccbb-355d-478d-95e4-05e5ac0c21f1/GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:53:38,714] [INFO] Task succeeded: fastANI
[2023-06-18 18:53:38,731] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:53:38,731] [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_009774615.1	s__Caccovicinus sp009774615	98.9486	912	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.13	99.13	0.87	0.87	2	conclusive
GCA_910584785.1	s__Caccovicinus sp910584785	84.8779	652	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575565.1	s__Caccovicinus sp910575565	77.9219	263	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.12	99.12	0.93	0.93	2	-
GCA_910589195.1	s__Caccovicinus sp910589195	77.4904	201	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713255.1	s__Caccovicinus excrementipullorum	77.2496	145	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.99	99.99	0.96	0.96	2	-
GCA_018715905.1	s__Caccovicinus merdipullorum	77.2483	150	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_017889125.1	s__Caccovicinus sp017889125	77.1701	167	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911065.1	s__Ventrimonas sp009911065	76.8237	109	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	95.78	95.73	0.75	0.73	3	-
GCA_003611875.1	s__Ventrimonas sp003611875	76.7344	117	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCF_900113155.1	s__Enterocloster clostridioformis	76.604	95	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.5883	84	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_018713185.1	s__Copromonas avistercoris	76.515	56	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	98.19	0.97	0.95	4	-
GCA_019118585.1	s__Enterocloster faecavium	76.5116	73	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.87	99.87	0.86	0.86	2	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	76.5107	83	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCF_002899675.1	s__CHH4-2 sp002899675	76.3739	87	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_910585645.1	s__UBA3402 sp910585645	76.3534	101	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577655.1	s__Ventrimonas sp910577655	76.2239	91	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389905.1	s__Lacrimispora sp002389905	76.1103	87	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:53:38,733] [INFO] GTDB search result was written to GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 18:53:38,733] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:53:38,737] [INFO] DFAST_QC result json was written to GCA_937889735.1_SRR4116674_bin.127_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 18:53:38,737] [INFO] DFAST_QC completed!
[2023-06-18 18:53:38,737] [INFO] Total running time: 0h1m12s