[2024-01-24 13:37:04,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:04,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:04,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference
[2024-01-24 13:37:06,414] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,415] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg1355ea63-00da-495e-b7c8-6838feba6783/GCF_000613645.1_ASM61364v1_genomic.fna.gz | prodigal -d GCF_000613645.1_ASM61364v1_genomic.fna/cds.fna -a GCF_000613645.1_ASM61364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:25,367] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:25,367] [INFO] Task started: HMMsearch
[2024-01-24 13:37:25,367] [INFO] Running command: hmmsearch --tblout GCF_000613645.1_ASM61364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference/reference_markers.hmm GCF_000613645.1_ASM61364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:25,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:25,720] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1355ea63-00da-495e-b7c8-6838feba6783/GCF_000613645.1_ASM61364v1_genomic.fna.gz]
[2024-01-24 13:37:25,763] [INFO] Query marker FASTA was written to GCF_000613645.1_ASM61364v1_genomic.fna/markers.fasta
[2024-01-24 13:37:25,770] [INFO] Task started: Blastn
[2024-01-24 13:37:25,771] [INFO] Running command: blastn -query GCF_000613645.1_ASM61364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference/reference_markers.fasta -out GCF_000613645.1_ASM61364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:26,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:26,490] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:26,490] [INFO] Target genome list was writen to GCF_000613645.1_ASM61364v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:26,497] [INFO] Task started: fastANI
[2024-01-24 13:37:26,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg1355ea63-00da-495e-b7c8-6838feba6783/GCF_000613645.1_ASM61364v1_genomic.fna.gz --refList GCF_000613645.1_ASM61364v1_genomic.fna/target_genomes.txt --output GCF_000613645.1_ASM61364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:39,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:39,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:39,136] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:39,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:39,136] [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
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	100.0	1179	1180	95	conclusive
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	99.9467	1170	1180	95	conclusive
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	80.7418	311	1180	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	80.5817	394	1180	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.5383	400	1180	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.9722	294	1180	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	79.9643	156	1180	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.7349	192	1180	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.6865	175	1180	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.4132	377	1180	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.3834	388	1180	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	78.8994	199	1180	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	77.7487	231	1180	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	77.506	142	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,140] [INFO] DFAST Taxonomy check result was written to GCF_000613645.1_ASM61364v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:39,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:39,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:39,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference/checkm_data
[2024-01-24 13:37:39,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:39,182] [INFO] Task started: CheckM
[2024-01-24 13:37:39,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613645.1_ASM61364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613645.1_ASM61364v1_genomic.fna/checkm_input GCF_000613645.1_ASM61364v1_genomic.fna/checkm_result
[2024-01-24 13:38:35,818] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:35,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:35,838] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:35,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:35,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613645.1_ASM61364v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:35,839] [INFO] Task started: Blastn
[2024-01-24 13:38:35,840] [INFO] Running command: blastn -query GCF_000613645.1_ASM61364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51aaec39-9c2f-4737-9c57-e4f9ed35502b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613645.1_ASM61364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:36,706] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:36,710] [INFO] Selected 17 target genomes.
[2024-01-24 13:38:36,711] [INFO] Target genome list was writen to GCF_000613645.1_ASM61364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:36,745] [INFO] Task started: fastANI
[2024-01-24 13:38:36,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg1355ea63-00da-495e-b7c8-6838feba6783/GCF_000613645.1_ASM61364v1_genomic.fna.gz --refList GCF_000613645.1_ASM61364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613645.1_ASM61364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:47,352] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:47,370] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:47,370] [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_000374585.1	s__Phocaeicola barnesiae	99.9467	1170	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	conclusive
GCA_900551645.1	s__Phocaeicola sp900551645	88.8785	577	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.46	98.46	0.80	0.80	2	-
GCA_900553185.1	s__Phocaeicola sp900553185	83.713	504	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	81.2667	433	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_003437535.1	s__Phocaeicola plebeius_A	81.0597	402	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	80.577	450	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_013618865.1	s__Phocaeicola sp900541515	80.5696	398	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_000187895.1	s__Phocaeicola plebeius	80.5582	396	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_900128495.1	s__Phocaeicola ilei	80.0278	391	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_900551445.1	s__Phocaeicola sp900551445	79.8129	313	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.5584	304	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157915.1	s__Phocaeicola coprophilus	79.3738	388	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_000432735.1	s__Phocaeicola sp000432735	79.29	326	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCF_016899805.1	s__Phocaeicola gallinaceus	78.9867	274	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.20	97.80	0.80	0.74	12	-
GCA_900542985.1	s__Phocaeicola sp900542985	78.9704	242	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_000436795.1	s__Phocaeicola sp000436795	78.18	240	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCA_019120125.1	s__Phocaeicola excrementigallinarum	78.0203	259	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,372] [INFO] GTDB search result was written to GCF_000613645.1_ASM61364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:47,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:47,376] [INFO] DFAST_QC result json was written to GCF_000613645.1_ASM61364v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:47,376] [INFO] DFAST_QC completed!
[2024-01-24 13:38:47,377] [INFO] Total running time: 0h1m42s