[2023-03-17 05:59:13,006] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:13,006] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:13,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference
[2023-03-17 05:59:14,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:14,075] [INFO] Task started: Prodigal
[2023-03-17 05:59:14,075] [INFO] Running command: cat /var/lib/cwl/stg33267c97-6541-484c-b39d-bbede5a55535/OceanDNA-b4003.fa | prodigal -d OceanDNA-b4003/cds.fna -a OceanDNA-b4003/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:36,616] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:36,616] [INFO] Task started: HMMsearch
[2023-03-17 05:59:36,616] [INFO] Running command: hmmsearch --tblout OceanDNA-b4003/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference/reference_markers.hmm OceanDNA-b4003/protein.faa > /dev/null
[2023-03-17 05:59:36,820] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:36,821] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg33267c97-6541-484c-b39d-bbede5a55535/OceanDNA-b4003.fa]
[2023-03-17 05:59:36,844] [INFO] Query marker FASTA was written to OceanDNA-b4003/markers.fasta
[2023-03-17 05:59:36,845] [INFO] Task started: Blastn
[2023-03-17 05:59:36,845] [INFO] Running command: blastn -query OceanDNA-b4003/markers.fasta -db /var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference/reference_markers.fasta -out OceanDNA-b4003/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:37,370] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:37,371] [INFO] Selected 20 target genomes.
[2023-03-17 05:59:37,371] [INFO] Target genome list was writen to OceanDNA-b4003/target_genomes.txt
[2023-03-17 05:59:37,379] [INFO] Task started: fastANI
[2023-03-17 05:59:37,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg33267c97-6541-484c-b39d-bbede5a55535/OceanDNA-b4003.fa --refList OceanDNA-b4003/target_genomes.txt --output OceanDNA-b4003/fastani_result.tsv --threads 1
[2023-03-17 05:59:52,511] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:52,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:52,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:52,521] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:52,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:59:52,521] [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
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	93.8924	716	878	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	82.8732	605	878	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	79.2326	158	878	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	78.2774	156	878	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	77.9641	131	878	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	77.9325	138	878	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.0585	82	878	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	77.0484	73	878	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.0272	83	878	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.0107	117	878	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	76.9587	57	878	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	76.7949	120	878	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.7876	136	878	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.6206	92	878	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	76.5527	59	878	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.5498	63	878	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	76.5263	79	878	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:59:52,521] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4003/tc_result.tsv
[2023-03-17 05:59:52,521] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:52,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:52,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference/checkm_data
[2023-03-17 05:59:52,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:52,590] [INFO] Task started: CheckM
[2023-03-17 05:59:52,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4003/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4003/checkm_input OceanDNA-b4003/checkm_result
[2023-03-17 06:00:50,876] [INFO] Task succeeded: CheckM
[2023-03-17 06:00:50,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.98%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:00:50,879] [INFO] ===== Completeness check finished =====
[2023-03-17 06:00:50,879] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:00:50,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4003/markers.fasta)
[2023-03-17 06:00:50,880] [INFO] Task started: Blastn
[2023-03-17 06:00:50,880] [INFO] Running command: blastn -query OceanDNA-b4003/markers.fasta -db /var/lib/cwl/stgf3d67e04-65e3-465b-b534-1ccf9d39db5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4003/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:00:51,600] [INFO] Task succeeded: Blastn
[2023-03-17 06:00:51,601] [INFO] Selected 23 target genomes.
[2023-03-17 06:00:51,601] [INFO] Target genome list was writen to OceanDNA-b4003/target_genomes_gtdb.txt
[2023-03-17 06:00:51,793] [INFO] Task started: fastANI
[2023-03-17 06:00:51,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg33267c97-6541-484c-b39d-bbede5a55535/OceanDNA-b4003.fa --refList OceanDNA-b4003/target_genomes_gtdb.txt --output OceanDNA-b4003/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:01:09,205] [INFO] Task succeeded: fastANI
[2023-03-17 06:01:09,217] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:01:09,217] [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_014652135.1	s__Mongoliitalea lutea	93.8924	716	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	79.2322	157	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	78.2774	156	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	77.9641	131	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	77.9325	138	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	77.7894	148	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	77.6817	119	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCA_003797895.1	s__Cecembia sp003797895	77.1692	104	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	77.0484	73	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.0272	83	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015476655.1	s__Aquiflexum lacus	77.0107	117	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	76.964	62	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	76.9587	57	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	76.9334	50	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.8646	103	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.8353	117	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	76.7444	138	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655305.1	s__Algoriphagus sp007655305	76.6446	91	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	76.5538	78	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841125.1	s__Echinicola sp014841125	76.5527	59	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.5498	63	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:01:09,217] [INFO] GTDB search result was written to OceanDNA-b4003/result_gtdb.tsv
[2023-03-17 06:01:09,217] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:01:09,219] [INFO] DFAST_QC result json was written to OceanDNA-b4003/dqc_result.json
[2023-03-17 06:01:09,219] [INFO] DFAST_QC completed!
[2023-03-17 06:01:09,219] [INFO] Total running time: 0h1m56s