[2023-06-30 14:11:23,279] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:11:23,281] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:11:23,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference
[2023-06-30 14:11:24,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:11:24,503] [INFO] Task started: Prodigal
[2023-06-30 14:11:24,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg32b5a035-77b7-4af0-a0df-9140f6a77a98/GCA_900764775.1_SRS255708_9_genomic.fna.gz | prodigal -d GCA_900764775.1_SRS255708_9_genomic.fna/cds.fna -a GCA_900764775.1_SRS255708_9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:11:45,648] [INFO] Task succeeded: Prodigal
[2023-06-30 14:11:45,649] [INFO] Task started: HMMsearch
[2023-06-30 14:11:45,649] [INFO] Running command: hmmsearch --tblout GCA_900764775.1_SRS255708_9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference/reference_markers.hmm GCA_900764775.1_SRS255708_9_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:11:45,929] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:11:45,931] [INFO] Found 6/6 markers.
[2023-06-30 14:11:45,971] [INFO] Query marker FASTA was written to GCA_900764775.1_SRS255708_9_genomic.fna/markers.fasta
[2023-06-30 14:11:45,971] [INFO] Task started: Blastn
[2023-06-30 14:11:45,971] [INFO] Running command: blastn -query GCA_900764775.1_SRS255708_9_genomic.fna/markers.fasta -db /var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference/reference_markers.fasta -out GCA_900764775.1_SRS255708_9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:11:46,574] [INFO] Task succeeded: Blastn
[2023-06-30 14:11:46,579] [INFO] Selected 14 target genomes.
[2023-06-30 14:11:46,579] [INFO] Target genome list was writen to GCA_900764775.1_SRS255708_9_genomic.fna/target_genomes.txt
[2023-06-30 14:11:46,582] [INFO] Task started: fastANI
[2023-06-30 14:11:46,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b5a035-77b7-4af0-a0df-9140f6a77a98/GCA_900764775.1_SRS255708_9_genomic.fna.gz --refList GCA_900764775.1_SRS255708_9_genomic.fna/target_genomes.txt --output GCA_900764775.1_SRS255708_9_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:11:58,206] [INFO] Task succeeded: fastANI
[2023-06-30 14:11:58,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:11:58,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:11:58,224] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-06-30 14:11:58,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 14:11:58,224] [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 ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	95.5515	789	1386	95	conclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	95.508	796	1386	95	conclusive
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	93.5282	482	1386	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	92.6117	713	1386	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	91.0858	399	1386	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	90.9812	398	1386	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	90.8739	399	1386	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	90.7863	403	1386	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	89.3916	517	1386	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	89.3911	516	1386	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	89.328	520	1386	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	89.235	526	1386	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	82.6347	399	1386	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	81.5684	447	1386	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:11:58,226] [INFO] DFAST Taxonomy check result was written to GCA_900764775.1_SRS255708_9_genomic.fna/tc_result.tsv
[2023-06-30 14:11:58,226] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:11:58,227] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:11:58,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference/checkm_data
[2023-06-30 14:11:58,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:11:58,268] [INFO] Task started: CheckM
[2023-06-30 14:11:58,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900764775.1_SRS255708_9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900764775.1_SRS255708_9_genomic.fna/checkm_input GCA_900764775.1_SRS255708_9_genomic.fna/checkm_result
[2023-06-30 14:12:59,562] [INFO] Task succeeded: CheckM
[2023-06-30 14:12:59,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 10.61%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 14:12:59,593] [INFO] ===== Completeness check finished =====
[2023-06-30 14:12:59,593] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:12:59,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900764775.1_SRS255708_9_genomic.fna/markers.fasta)
[2023-06-30 14:12:59,594] [INFO] Task started: Blastn
[2023-06-30 14:12:59,594] [INFO] Running command: blastn -query GCA_900764775.1_SRS255708_9_genomic.fna/markers.fasta -db /var/lib/cwl/stg67082503-ffd7-4384-b055-219d65b75ab5/dqc_reference/reference_markers_gtdb.fasta -out GCA_900764775.1_SRS255708_9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:13:00,471] [INFO] Task succeeded: Blastn
[2023-06-30 14:13:00,477] [INFO] Selected 15 target genomes.
[2023-06-30 14:13:00,477] [INFO] Target genome list was writen to GCA_900764775.1_SRS255708_9_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:13:00,484] [INFO] Task started: fastANI
[2023-06-30 14:13:00,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b5a035-77b7-4af0-a0df-9140f6a77a98/GCA_900764775.1_SRS255708_9_genomic.fna.gz --refList GCA_900764775.1_SRS255708_9_genomic.fna/target_genomes_gtdb.txt --output GCA_900764775.1_SRS255708_9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:13:13,848] [INFO] Task succeeded: fastANI
[2023-06-30 14:13:13,865] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:13:13,865] [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_001314995.1	s__Bacteroides ovatus	95.5857	791	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	conclusive
GCF_000210075.1	s__Bacteroides xylanisolvens	92.5861	714	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	92.5215	734	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_000154205.1	s__Bacteroides uniformis	90.931	397	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCA_902362375.1	s__Bacteroides sp902362375	90.915	692	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_009193295.2	s__Bacteroides luhongzhouii	90.4963	624	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_001688725.2	s__Bacteroides caecimuris	89.328	520	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_000614125.1	s__Bacteroides rodentium	88.8022	348	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	87.1472	347	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_900755095.1	s__Bacteroides sp900755095	86.693	263	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	80.1905	288	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	80.0585	261	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000154525.1	s__Bacteroides stercoris	80.0387	294	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_019129285.1	s__Bacteroides sp900552405	79.8246	278	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_003438615.1	s__Bacteroides sp003545565	79.2238	263	1386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2023-06-30 14:13:13,868] [INFO] GTDB search result was written to GCA_900764775.1_SRS255708_9_genomic.fna/result_gtdb.tsv
[2023-06-30 14:13:13,868] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:13:13,875] [INFO] DFAST_QC result json was written to GCA_900764775.1_SRS255708_9_genomic.fna/dqc_result.json
[2023-06-30 14:13:13,875] [INFO] DFAST_QC completed!
[2023-06-30 14:13:13,876] [INFO] Total running time: 0h1m51s