[2023-06-05 18:02:42,466] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:02:42,485] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:02:42,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference
[2023-06-05 18:02:43,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:02:43,982] [INFO] Task started: Prodigal
[2023-06-05 18:02:43,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dcda101-9814-4e1c-b489-1dfc17435c68/GCA_934852795.1_MTG235_bin.31.fa_genomic.fna.gz | prodigal -d GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/cds.fna -a GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:49,194] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:49,194] [INFO] Task started: HMMsearch
[2023-06-05 18:02:49,194] [INFO] Running command: hmmsearch --tblout GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference/reference_markers.hmm GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:49,426] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:49,427] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5dcda101-9814-4e1c-b489-1dfc17435c68/GCA_934852795.1_MTG235_bin.31.fa_genomic.fna.gz]
[2023-06-05 18:02:49,450] [INFO] Query marker FASTA was written to GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/markers.fasta
[2023-06-05 18:02:49,450] [INFO] Task started: Blastn
[2023-06-05 18:02:49,450] [INFO] Running command: blastn -query GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference/reference_markers.fasta -out GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:50,035] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:50,039] [INFO] Selected 16 target genomes.
[2023-06-05 18:02:50,039] [INFO] Target genome list was writen to GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/target_genomes.txt
[2023-06-05 18:02:50,041] [INFO] Task started: fastANI
[2023-06-05 18:02:50,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dcda101-9814-4e1c-b489-1dfc17435c68/GCA_934852795.1_MTG235_bin.31.fa_genomic.fna.gz --refList GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/target_genomes.txt --output GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:02:58,694] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:58,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:02:58,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:02:58,705] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:02:58,705] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:02:58,705] [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
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.2783	91	649	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.9982	62	649	95	below_threshold
Blautia producta	strain=JCM 1471	GCA_010669205.1	33035	33035	suspected-type	True	76.9435	69	649	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	76.9163	70	649	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.9096	70	649	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	76.8805	71	649	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.5019	65	649	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.4825	67	649	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.4825	67	649	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:02:58,707] [INFO] DFAST Taxonomy check result was written to GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/tc_result.tsv
[2023-06-05 18:02:58,708] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:02:58,708] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:02:58,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference/checkm_data
[2023-06-05 18:02:58,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:02:58,749] [INFO] Task started: CheckM
[2023-06-05 18:02:58,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/checkm_input GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/checkm_result
[2023-06-05 18:03:29,242] [INFO] Task succeeded: CheckM
[2023-06-05 18:03:29,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:03:29,320] [INFO] ===== Completeness check finished =====
[2023-06-05 18:03:29,320] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:03:29,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/markers.fasta)
[2023-06-05 18:03:29,321] [INFO] Task started: Blastn
[2023-06-05 18:03:29,321] [INFO] Running command: blastn -query GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg42ca558e-8eef-491b-b497-bb5ced419ced/dqc_reference/reference_markers_gtdb.fasta -out GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:03:30,326] [INFO] Task succeeded: Blastn
[2023-06-05 18:03:30,331] [INFO] Selected 13 target genomes.
[2023-06-05 18:03:30,331] [INFO] Target genome list was writen to GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:03:30,337] [INFO] Task started: fastANI
[2023-06-05 18:03:30,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dcda101-9814-4e1c-b489-1dfc17435c68/GCA_934852795.1_MTG235_bin.31.fa_genomic.fna.gz --refList GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:03:40,263] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:40,272] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:03:40,272] [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
GCF_015557635.1	s__Fusicatenibacter saccharivorans	98.1617	617	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	97.82	97.27	0.86	0.77	91	conclusive
GCA_900772675.1	s__Fusicatenibacter sp900772675	89.9784	301	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899975.1	s__Fusicatenibacter sp900543115	78.7169	140	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	98.27	97.10	0.88	0.78	8	-
GCA_017887445.1	s__Fusicatenibacter sp017887445	77.7499	130	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119555.1	s__Fusicatenibacter intestinigallinarum	77.6824	100	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	99.96	99.96	0.92	0.92	2	-
GCA_019115005.1	s__Fusicatenibacter merdavium	77.5781	97	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	99.43	98.88	0.95	0.93	3	-
GCA_002361775.1	s__Oliverpabstia sp002361775	77.3696	55	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCA_018713585.1	s__Pullilachnospira stercoravium	76.3919	59	649	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	-
--------------------------------------------------------------------------------
[2023-06-05 18:03:40,275] [INFO] GTDB search result was written to GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 18:03:40,275] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:03:40,279] [INFO] DFAST_QC result json was written to GCA_934852795.1_MTG235_bin.31.fa_genomic.fna/dqc_result.json
[2023-06-05 18:03:40,279] [INFO] DFAST_QC completed!
[2023-06-05 18:03:40,279] [INFO] Total running time: 0h0m58s