[2024-01-25 19:52:35,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:35,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:35,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference
[2024-01-25 19:52:36,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:36,758] [INFO] Task started: Prodigal
[2024-01-25 19:52:36,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fab3c24-d940-40a5-949a-997fa86d0eb5/GCF_013618865.1_ASM1361886v1_genomic.fna.gz | prodigal -d GCF_013618865.1_ASM1361886v1_genomic.fna/cds.fna -a GCF_013618865.1_ASM1361886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:55,714] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:55,714] [INFO] Task started: HMMsearch
[2024-01-25 19:52:55,714] [INFO] Running command: hmmsearch --tblout GCF_013618865.1_ASM1361886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference/reference_markers.hmm GCF_013618865.1_ASM1361886v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:56,003] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:56,004] [INFO] Found 6/6 markers.
[2024-01-25 19:52:56,051] [INFO] Query marker FASTA was written to GCF_013618865.1_ASM1361886v1_genomic.fna/markers.fasta
[2024-01-25 19:52:56,051] [INFO] Task started: Blastn
[2024-01-25 19:52:56,051] [INFO] Running command: blastn -query GCF_013618865.1_ASM1361886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference/reference_markers.fasta -out GCF_013618865.1_ASM1361886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:56,617] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:56,623] [INFO] Selected 16 target genomes.
[2024-01-25 19:52:56,624] [INFO] Target genome list was writen to GCF_013618865.1_ASM1361886v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:56,653] [INFO] Task started: fastANI
[2024-01-25 19:52:56,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fab3c24-d940-40a5-949a-997fa86d0eb5/GCF_013618865.1_ASM1361886v1_genomic.fna.gz --refList GCF_013618865.1_ASM1361886v1_genomic.fna/target_genomes.txt --output GCF_013618865.1_ASM1361886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:07,276] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:07,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:07,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:07,287] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:53:07,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:07,287] [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 faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	100.0	1417	1423	95	conclusive
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	82.0014	402	1423	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	81.9702	379	1423	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	81.9126	122	1423	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	81.2456	383	1423	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	81.2036	370	1423	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	80.822	384	1423	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	80.7008	393	1423	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	80.3627	51	1423	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	79.7957	242	1423	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.739	178	1423	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	78.1157	115	1423	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_002998435.1	28119	28119	type	True	77.975	119	1423	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.9478	54	1423	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.9316	56	1423	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.7322	53	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:07,289] [INFO] DFAST Taxonomy check result was written to GCF_013618865.1_ASM1361886v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:07,290] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:07,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:07,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference/checkm_data
[2024-01-25 19:53:07,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:07,347] [INFO] Task started: CheckM
[2024-01-25 19:53:07,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013618865.1_ASM1361886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013618865.1_ASM1361886v1_genomic.fna/checkm_input GCF_013618865.1_ASM1361886v1_genomic.fna/checkm_result
[2024-01-25 19:54:01,428] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:01,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:01,456] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:01,456] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:01,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013618865.1_ASM1361886v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:01,457] [INFO] Task started: Blastn
[2024-01-25 19:54:01,457] [INFO] Running command: blastn -query GCF_013618865.1_ASM1361886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2709b972-95c5-4fdb-b0bd-00146843580f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013618865.1_ASM1361886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:02,362] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:02,365] [INFO] Selected 19 target genomes.
[2024-01-25 19:54:02,365] [INFO] Target genome list was writen to GCF_013618865.1_ASM1361886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:02,392] [INFO] Task started: fastANI
[2024-01-25 19:54:02,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fab3c24-d940-40a5-949a-997fa86d0eb5/GCF_013618865.1_ASM1361886v1_genomic.fna.gz --refList GCF_013618865.1_ASM1361886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013618865.1_ASM1361886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:13,538] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:13,548] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:13,549] [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_013618865.1	s__Phocaeicola sp900541515	100.0	1417	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	conclusive
GCF_000187895.1	s__Phocaeicola plebeius	82.0082	402	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_000157915.1	s__Phocaeicola coprophilus	81.2467	383	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	80.8688	415	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_000374585.1	s__Phocaeicola barnesiae	80.7474	389	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_003437535.1	s__Phocaeicola plebeius_A	80.6859	367	1423	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	80.1427	403	1423	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	79.8546	371	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCA_000432735.1	s__Phocaeicola sp000432735	79.7471	350	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCA_900553185.1	s__Phocaeicola sp900553185	79.3949	232	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCA_900556845.1	s__Phocaeicola sp900556845	79.3556	155	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.3053	269	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.2711	253	1423	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	78.3697	276	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCA_019249655.1	s__Prevotella sp900767615	77.3358	76	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCA_017558175.1	s__Phocaeicola sp017558175	77.2164	92	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:13,550] [INFO] GTDB search result was written to GCF_013618865.1_ASM1361886v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:13,551] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:13,554] [INFO] DFAST_QC result json was written to GCF_013618865.1_ASM1361886v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:13,554] [INFO] DFAST_QC completed!
[2024-01-25 19:54:13,554] [INFO] Total running time: 0h1m38s