[2024-01-24 14:06:30,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference
[2024-01-24 14:06:32,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,382] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,383] [INFO] Running command: gunzip -c /var/lib/cwl/stg73f4e4b0-c033-4110-93d7-89c73ff168a2/GCF_900108345.1_PRJEB16738_genomic.fna.gz | prodigal -d GCF_900108345.1_PRJEB16738_genomic.fna/cds.fna -a GCF_900108345.1_PRJEB16738_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:00,122] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:00,123] [INFO] Task started: HMMsearch
[2024-01-24 14:07:00,123] [INFO] Running command: hmmsearch --tblout GCF_900108345.1_PRJEB16738_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference/reference_markers.hmm GCF_900108345.1_PRJEB16738_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:00,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:00,419] [INFO] Found 6/6 markers.
[2024-01-24 14:07:00,460] [INFO] Query marker FASTA was written to GCF_900108345.1_PRJEB16738_genomic.fna/markers.fasta
[2024-01-24 14:07:00,460] [INFO] Task started: Blastn
[2024-01-24 14:07:00,460] [INFO] Running command: blastn -query GCF_900108345.1_PRJEB16738_genomic.fna/markers.fasta -db /var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference/reference_markers.fasta -out GCF_900108345.1_PRJEB16738_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:01,106] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:01,109] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:01,109] [INFO] Target genome list was writen to GCF_900108345.1_PRJEB16738_genomic.fna/target_genomes.txt
[2024-01-24 14:07:01,124] [INFO] Task started: fastANI
[2024-01-24 14:07:01,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f4e4b0-c033-4110-93d7-89c73ff168a2/GCF_900108345.1_PRJEB16738_genomic.fna.gz --refList GCF_900108345.1_PRJEB16738_genomic.fna/target_genomes.txt --output GCF_900108345.1_PRJEB16738_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:14,625] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:14,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:14,643] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:14,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:14,643] [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
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	81.3026	417	1644	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	81.2658	217	1644	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	81.2579	420	1644	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	81.1647	416	1644	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	80.2271	377	1644	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	80.1756	376	1644	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	80.0783	369	1644	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.8759	404	1644	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	79.7949	395	1644	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	79.7281	400	1644	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	79.5186	380	1644	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.507	393	1644	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.3138	360	1644	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.1769	386	1644	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	78.9674	382	1644	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	78.9511	350	1644	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	78.9098	354	1644	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.8199	375	1644	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	78.7362	360	1644	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	78.637	296	1644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,647] [INFO] DFAST Taxonomy check result was written to GCF_900108345.1_PRJEB16738_genomic.fna/tc_result.tsv
[2024-01-24 14:07:14,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:14,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:14,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference/checkm_data
[2024-01-24 14:07:14,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:14,729] [INFO] Task started: CheckM
[2024-01-24 14:07:14,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108345.1_PRJEB16738_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108345.1_PRJEB16738_genomic.fna/checkm_input GCF_900108345.1_PRJEB16738_genomic.fna/checkm_result
[2024-01-24 14:08:30,596] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:30,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:30,618] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:30,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:30,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108345.1_PRJEB16738_genomic.fna/markers.fasta)
[2024-01-24 14:08:30,620] [INFO] Task started: Blastn
[2024-01-24 14:08:30,620] [INFO] Running command: blastn -query GCF_900108345.1_PRJEB16738_genomic.fna/markers.fasta -db /var/lib/cwl/stg057dd1b9-77ce-44f2-8011-5067b63cfa98/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108345.1_PRJEB16738_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:31,515] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:31,518] [INFO] Selected 17 target genomes.
[2024-01-24 14:08:31,518] [INFO] Target genome list was writen to GCF_900108345.1_PRJEB16738_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:31,537] [INFO] Task started: fastANI
[2024-01-24 14:08:31,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f4e4b0-c033-4110-93d7-89c73ff168a2/GCF_900108345.1_PRJEB16738_genomic.fna.gz --refList GCF_900108345.1_PRJEB16738_genomic.fna/target_genomes_gtdb.txt --output GCF_900108345.1_PRJEB16738_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:45,816] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:45,832] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:45,833] [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_900108345.1	s__Bacteroides ndongoniae	100.0	1643	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	conclusive
GCA_905201685.1	s__Bacteroides sp905201685	87.8556	473	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128475.1	s__Bacteroides massiliensis	82.0621	611	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCF_900130135.1	s__Bacteroides togonis	81.3284	528	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_000374365.1	s__Bacteroides gallinarum	81.2422	421	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_019116805.1	s__Bacteroides merdavium	80.3631	426	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154205.1	s__Bacteroides uniformis	79.7359	402	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000614125.1	s__Bacteroides rodentium	79.2379	436	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154525.1	s__Bacteroides stercoris	78.989	382	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCA_902388495.1	s__Bacteroides sp902388495	78.9427	344	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900129655.1	s__Bacteroides clarus	78.9378	351	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000195635.1	s__Bacteroides fluxus	78.7595	358	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_000186225.1	s__Bacteroides helcogenes	78.6287	297	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578895.1	s__Bacteroides sp910578895	78.6262	356	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342845.1	s__Bacteroides heparinolyticus	78.3497	307	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCA_017471925.1	s__Bacteroides sp017471925	77.7912	258	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557355.1	s__Bacteroides sp900557355	76.4919	124	1644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	98.57	0.54	0.54	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:45,834] [INFO] GTDB search result was written to GCF_900108345.1_PRJEB16738_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:45,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:45,839] [INFO] DFAST_QC result json was written to GCF_900108345.1_PRJEB16738_genomic.fna/dqc_result.json
[2024-01-24 14:08:45,839] [INFO] DFAST_QC completed!
[2024-01-24 14:08:45,839] [INFO] Total running time: 0h2m15s