[2023-06-13 19:16:25,213] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:16:25,214] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:16:25,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference
[2023-06-13 19:16:26,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:16:26,369] [INFO] Task started: Prodigal
[2023-06-13 19:16:26,370] [INFO] Running command: gunzip -c /var/lib/cwl/stg002d76ac-9efb-4b36-a874-f37f9335fb36/GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:16:31,255] [INFO] Task succeeded: Prodigal
[2023-06-13 19:16:31,256] [INFO] Task started: HMMsearch
[2023-06-13 19:16:31,256] [INFO] Running command: hmmsearch --tblout GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference/reference_markers.hmm GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:16:31,436] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:16:31,437] [INFO] Found 6/6 markers.
[2023-06-13 19:16:31,459] [INFO] Query marker FASTA was written to GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 19:16:31,459] [INFO] Task started: Blastn
[2023-06-13 19:16:31,459] [INFO] Running command: blastn -query GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference/reference_markers.fasta -out GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:16:32,146] [INFO] Task succeeded: Blastn
[2023-06-13 19:16:32,150] [INFO] Selected 21 target genomes.
[2023-06-13 19:16:32,151] [INFO] Target genome list was writen to GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 19:16:32,152] [INFO] Task started: fastANI
[2023-06-13 19:16:32,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg002d76ac-9efb-4b36-a874-f37f9335fb36/GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:16:40,773] [INFO] Task succeeded: fastANI
[2023-06-13 19:16:40,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:16:40,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:16:40,784] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:16:40,784] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:16:40,784] [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
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.7367	99	574	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.6208	113	574	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.3959	100	574	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.8816	90	574	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.8545	71	574	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.7483	70	574	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.723	67	574	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.7139	64	574	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.5836	81	574	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.5309	56	574	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:16:40,786] [INFO] DFAST Taxonomy check result was written to GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 19:16:40,787] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:16:40,787] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:16:40,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference/checkm_data
[2023-06-13 19:16:40,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:16:40,810] [INFO] Task started: CheckM
[2023-06-13 19:16:40,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 19:17:00,883] [INFO] Task succeeded: CheckM
[2023-06-13 19:17:00,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:17:00,906] [INFO] ===== Completeness check finished =====
[2023-06-13 19:17:00,906] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:17:00,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 19:17:00,907] [INFO] Task started: Blastn
[2023-06-13 19:17:00,907] [INFO] Running command: blastn -query GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6147fbaa-c434-43ee-a5ea-bcdfc740a2e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:17:02,172] [INFO] Task succeeded: Blastn
[2023-06-13 19:17:02,175] [INFO] Selected 10 target genomes.
[2023-06-13 19:17:02,176] [INFO] Target genome list was writen to GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:17:02,178] [INFO] Task started: fastANI
[2023-06-13 19:17:02,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg002d76ac-9efb-4b36-a874-f37f9335fb36/GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:17:06,586] [INFO] Task succeeded: fastANI
[2023-06-13 19:17:06,600] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:17:06,601] [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_900552015.1	s__ER4 sp900552015	100.0	544	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_900763705.1	s__ER4 sp900763705	90.9712	334	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765235.1	s__ER4 sp000765235	90.7285	436	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.82	96.40	0.83	0.70	19	-
GCA_900550165.1	s__ER4 sp900550165	90.646	407	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.79	96.53	0.85	0.84	4	-
GCA_900546295.1	s__ER4 sp900546295	90.0566	372	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.01	98.01	0.87	0.87	2	-
GCA_900556145.1	s__ER4 sp900556145	88.4495	249	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003522105.1	s__ER4 sp003522105	87.3971	350	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.35	97.09	0.78	0.74	7	-
GCA_002405995.1	s__ER4 sp002405995	85.3581	332	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_900549405.1	s__Lawsonibacter sp900549405	77.3982	78	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-13 19:17:06,603] [INFO] GTDB search result was written to GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 19:17:06,603] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:17:06,607] [INFO] DFAST_QC result json was written to GCA_938048985.1_ERR1305885_bin.6_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 19:17:06,607] [INFO] DFAST_QC completed!
[2023-06-13 19:17:06,607] [INFO] Total running time: 0h0m41s