[2023-07-01 03:00:33,873] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:00:33,876] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:00:33,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference
[2023-07-01 03:00:35,097] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:00:35,098] [INFO] Task started: Prodigal
[2023-07-01 03:00:35,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg4742500f-7827-4dd7-8975-d7eace80df2e/GCA_025543655.1_ASM2554365v1_genomic.fna.gz | prodigal -d GCA_025543655.1_ASM2554365v1_genomic.fna/cds.fna -a GCA_025543655.1_ASM2554365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:00:54,653] [INFO] Task succeeded: Prodigal
[2023-07-01 03:00:54,654] [INFO] Task started: HMMsearch
[2023-07-01 03:00:54,654] [INFO] Running command: hmmsearch --tblout GCA_025543655.1_ASM2554365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference/reference_markers.hmm GCA_025543655.1_ASM2554365v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:00:54,926] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:00:54,927] [INFO] Found 6/6 markers.
[2023-07-01 03:00:54,958] [INFO] Query marker FASTA was written to GCA_025543655.1_ASM2554365v1_genomic.fna/markers.fasta
[2023-07-01 03:00:54,959] [INFO] Task started: Blastn
[2023-07-01 03:00:54,959] [INFO] Running command: blastn -query GCA_025543655.1_ASM2554365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference/reference_markers.fasta -out GCA_025543655.1_ASM2554365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:00:55,578] [INFO] Task succeeded: Blastn
[2023-07-01 03:00:55,582] [INFO] Selected 11 target genomes.
[2023-07-01 03:00:55,583] [INFO] Target genome list was writen to GCA_025543655.1_ASM2554365v1_genomic.fna/target_genomes.txt
[2023-07-01 03:00:55,584] [INFO] Task started: fastANI
[2023-07-01 03:00:55,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg4742500f-7827-4dd7-8975-d7eace80df2e/GCA_025543655.1_ASM2554365v1_genomic.fna.gz --refList GCA_025543655.1_ASM2554365v1_genomic.fna/target_genomes.txt --output GCA_025543655.1_ASM2554365v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:01:03,447] [INFO] Task succeeded: fastANI
[2023-07-01 03:01:03,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:01:03,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:01:03,461] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:01:03,461] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:01:03,461] [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 plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	93.9204	925	1232	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.3468	357	1232	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	80.0268	375	1232	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.9889	393	1232	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.6646	359	1232	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.6497	356	1232	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.224	175	1232	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.9425	275	1232	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	78.6275	252	1232	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	78.6195	263	1232	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.2492	163	1232	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:01:03,464] [INFO] DFAST Taxonomy check result was written to GCA_025543655.1_ASM2554365v1_genomic.fna/tc_result.tsv
[2023-07-01 03:01:03,464] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:01:03,464] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:01:03,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference/checkm_data
[2023-07-01 03:01:03,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:01:03,524] [INFO] Task started: CheckM
[2023-07-01 03:01:03,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025543655.1_ASM2554365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025543655.1_ASM2554365v1_genomic.fna/checkm_input GCA_025543655.1_ASM2554365v1_genomic.fna/checkm_result
[2023-07-01 03:02:00,541] [INFO] Task succeeded: CheckM
[2023-07-01 03:02:00,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:02:00,566] [INFO] ===== Completeness check finished =====
[2023-07-01 03:02:00,566] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:02:00,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025543655.1_ASM2554365v1_genomic.fna/markers.fasta)
[2023-07-01 03:02:00,567] [INFO] Task started: Blastn
[2023-07-01 03:02:00,567] [INFO] Running command: blastn -query GCA_025543655.1_ASM2554365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb54d03-36f1-4887-a7f6-a5011c221d86/dqc_reference/reference_markers_gtdb.fasta -out GCA_025543655.1_ASM2554365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:02:01,423] [INFO] Task succeeded: Blastn
[2023-07-01 03:02:01,428] [INFO] Selected 7 target genomes.
[2023-07-01 03:02:01,428] [INFO] Target genome list was writen to GCA_025543655.1_ASM2554365v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:02:01,433] [INFO] Task started: fastANI
[2023-07-01 03:02:01,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg4742500f-7827-4dd7-8975-d7eace80df2e/GCA_025543655.1_ASM2554365v1_genomic.fna.gz --refList GCA_025543655.1_ASM2554365v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025543655.1_ASM2554365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:02:07,200] [INFO] Task succeeded: fastANI
[2023-07-01 03:02:07,211] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:02:07,211] [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_003437535.1	s__Phocaeicola plebeius_A	97.9896	1035	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	conclusive
GCF_000187895.1	s__Phocaeicola plebeius	93.9204	925	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	83.925	764	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	83.8039	791	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_016900355.1	s__Phocaeicola sp900551065	83.515	732	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCA_900552075.1	s__Phocaeicola sp900552075	83.4403	559	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551445.1	s__Phocaeicola sp900551445	83.4092	606	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
--------------------------------------------------------------------------------
[2023-07-01 03:02:07,213] [INFO] GTDB search result was written to GCA_025543655.1_ASM2554365v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:02:07,213] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:02:07,217] [INFO] DFAST_QC result json was written to GCA_025543655.1_ASM2554365v1_genomic.fna/dqc_result.json
[2023-07-01 03:02:07,217] [INFO] DFAST_QC completed!
[2023-07-01 03:02:07,217] [INFO] Total running time: 0h1m33s