[2023-03-15 08:55:06,627] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference
[2023-03-15 08:55:08,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,347] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,348] [INFO] Running command: cat /var/lib/cwl/stge77ae7a3-3741-41e8-9a4e-eeb6fd210067/OceanDNA-b3470.fa | prodigal -d OceanDNA-b3470/cds.fna -a OceanDNA-b3470/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:33,439] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:33,439] [INFO] Task started: HMMsearch
[2023-03-15 08:55:33,439] [INFO] Running command: hmmsearch --tblout OceanDNA-b3470/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference/reference_markers.hmm OceanDNA-b3470/protein.faa > /dev/null
[2023-03-15 08:55:33,758] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:33,758] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge77ae7a3-3741-41e8-9a4e-eeb6fd210067/OceanDNA-b3470.fa]
[2023-03-15 08:55:33,781] [INFO] Query marker FASTA was written to OceanDNA-b3470/markers.fasta
[2023-03-15 08:55:33,781] [INFO] Task started: Blastn
[2023-03-15 08:55:33,781] [INFO] Running command: blastn -query OceanDNA-b3470/markers.fasta -db /var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference/reference_markers.fasta -out OceanDNA-b3470/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:34,365] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:34,366] [INFO] Selected 12 target genomes.
[2023-03-15 08:55:34,366] [INFO] Target genome list was writen to OceanDNA-b3470/target_genomes.txt
[2023-03-15 08:55:34,372] [INFO] Task started: fastANI
[2023-03-15 08:55:34,372] [INFO] Running command: fastANI --query /var/lib/cwl/stge77ae7a3-3741-41e8-9a4e-eeb6fd210067/OceanDNA-b3470.fa --refList OceanDNA-b3470/target_genomes.txt --output OceanDNA-b3470/fastani_result.tsv --threads 1
[2023-03-15 08:55:43,283] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:43,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:43,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:43,291] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:43,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:43,291] [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	93.5247	750	1001	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.9846	297	1001	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	80.2827	301	1001	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	80.2002	301	1001	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.9492	303	1001	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	79.9272	303	1001	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.3101	153	1001	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.2628	129	1001	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	78.6769	149	1001	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.3476	227	1001	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	78.1997	214	1001	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	78.0029	211	1001	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:43,292] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3470/tc_result.tsv
[2023-03-15 08:55:43,292] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:43,292] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:43,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference/checkm_data
[2023-03-15 08:55:43,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:43,298] [INFO] Task started: CheckM
[2023-03-15 08:55:43,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3470/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3470/checkm_input OceanDNA-b3470/checkm_result
[2023-03-15 08:56:47,114] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:47,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.33%
Contamintation: 11.28%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-15 08:56:47,117] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:47,118] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:47,118] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3470/markers.fasta)
[2023-03-15 08:56:47,119] [INFO] Task started: Blastn
[2023-03-15 08:56:47,119] [INFO] Running command: blastn -query OceanDNA-b3470/markers.fasta -db /var/lib/cwl/stgd30cdb3c-65a8-447e-90f8-5f132eb3ee61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3470/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:48,040] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:48,040] [INFO] Selected 7 target genomes.
[2023-03-15 08:56:48,040] [INFO] Target genome list was writen to OceanDNA-b3470/target_genomes_gtdb.txt
[2023-03-15 08:56:48,047] [INFO] Task started: fastANI
[2023-03-15 08:56:48,047] [INFO] Running command: fastANI --query /var/lib/cwl/stge77ae7a3-3741-41e8-9a4e-eeb6fd210067/OceanDNA-b3470.fa --refList OceanDNA-b3470/target_genomes_gtdb.txt --output OceanDNA-b3470/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:53,209] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:53,214] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:56:53,214] [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	98.6151	852	1001	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	93.5896	747	1001	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	83.6756	631	1001	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	83.462	607	1001	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	83.2815	576	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCA_900551445.1	s__Phocaeicola sp900551445	83.1781	493	1001	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	82.9616	460	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:53,214] [INFO] GTDB search result was written to OceanDNA-b3470/result_gtdb.tsv
[2023-03-15 08:56:53,214] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:53,215] [INFO] DFAST_QC result json was written to OceanDNA-b3470/dqc_result.json
[2023-03-15 08:56:53,215] [INFO] DFAST_QC completed!
[2023-03-15 08:56:53,215] [INFO] Total running time: 0h1m47s