[2023-03-14 15:01:55,968] [INFO] DFAST_QC pipeline started.
[2023-03-14 15:01:55,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 15:01:55,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference
[2023-03-14 15:01:59,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 15:01:59,389] [INFO] Task started: Prodigal
[2023-03-14 15:01:59,389] [INFO] Running command: cat /var/lib/cwl/stg9e9c5b5a-c5c8-47da-9204-815b867abfa5/OceanDNA-b7123.fa | prodigal -d OceanDNA-b7123/cds.fna -a OceanDNA-b7123/protein.faa -g 11 -q > /dev/null
[2023-03-14 15:02:16,664] [INFO] Task succeeded: Prodigal
[2023-03-14 15:02:16,664] [INFO] Task started: HMMsearch
[2023-03-14 15:02:16,664] [INFO] Running command: hmmsearch --tblout OceanDNA-b7123/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference/reference_markers.hmm OceanDNA-b7123/protein.faa > /dev/null
[2023-03-14 15:02:17,060] [INFO] Task succeeded: HMMsearch
[2023-03-14 15:02:17,061] [INFO] Found 6/6 markers.
[2023-03-14 15:02:17,075] [INFO] Query marker FASTA was written to OceanDNA-b7123/markers.fasta
[2023-03-14 15:02:17,082] [INFO] Task started: Blastn
[2023-03-14 15:02:17,082] [INFO] Running command: blastn -query OceanDNA-b7123/markers.fasta -db /var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference/reference_markers.fasta -out OceanDNA-b7123/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:02:18,476] [INFO] Task succeeded: Blastn
[2023-03-14 15:02:18,477] [INFO] Selected 31 target genomes.
[2023-03-14 15:02:18,477] [INFO] Target genome list was writen to OceanDNA-b7123/target_genomes.txt
[2023-03-14 15:02:18,524] [INFO] Task started: fastANI
[2023-03-14 15:02:18,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e9c5b5a-c5c8-47da-9204-815b867abfa5/OceanDNA-b7123.fa --refList OceanDNA-b7123/target_genomes.txt --output OceanDNA-b7123/fastani_result.tsv --threads 1
[2023-03-14 15:02:38,490] [INFO] Task succeeded: fastANI
[2023-03-14 15:02:38,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 15:02:38,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 15:02:38,497] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 15:02:38,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 15:02:38,497] [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
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	75.3583	50	623	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.2814	53	623	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.1877	68	623	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.0597	53	623	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	74.925	52	623	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 15:02:38,497] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7123/tc_result.tsv
[2023-03-14 15:02:38,497] [INFO] ===== Taxonomy check completed =====
[2023-03-14 15:02:38,497] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 15:02:38,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference/checkm_data
[2023-03-14 15:02:38,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 15:02:38,501] [INFO] Task started: CheckM
[2023-03-14 15:02:38,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7123/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7123/checkm_input OceanDNA-b7123/checkm_result
[2023-03-14 15:03:09,238] [INFO] Task succeeded: CheckM
[2023-03-14 15:03:09,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 15:03:09,241] [INFO] ===== Completeness check finished =====
[2023-03-14 15:03:09,241] [INFO] ===== Start GTDB Search =====
[2023-03-14 15:03:09,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7123/markers.fasta)
[2023-03-14 15:03:09,241] [INFO] Task started: Blastn
[2023-03-14 15:03:09,241] [INFO] Running command: blastn -query OceanDNA-b7123/markers.fasta -db /var/lib/cwl/stg9d211439-1728-428f-8cc3-45c74d1686c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7123/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:03:10,168] [INFO] Task succeeded: Blastn
[2023-03-14 15:03:10,169] [INFO] Selected 25 target genomes.
[2023-03-14 15:03:10,169] [INFO] Target genome list was writen to OceanDNA-b7123/target_genomes_gtdb.txt
[2023-03-14 15:03:10,352] [INFO] Task started: fastANI
[2023-03-14 15:03:10,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e9c5b5a-c5c8-47da-9204-815b867abfa5/OceanDNA-b7123.fa --refList OceanDNA-b7123/target_genomes_gtdb.txt --output OceanDNA-b7123/fastani_result_gtdb.tsv --threads 1
[2023-03-14 15:03:17,232] [INFO] Task succeeded: fastANI
[2023-03-14 15:03:17,243] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 15:03:17,243] [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
GCA_002719315.1	s__GCA-2719315 sp002719315	99.2617	612	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902560065.1	s__GCA-2719315 sp902560065	94.791	351	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728855.1	s__GCA-002728855 sp002728855	76.7442	115	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002728855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514625.1	s__TMED220 sp902514625	76.3853	85	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	76.2684	85	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_002721275.1	s__GCA-002723295 sp002721275	76.158	85	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517245.1	s__MS024-2A sp902517245	76.1476	72	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713495.1	s__GCA-002723295 sp002713495	76.0048	94	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	75.9841	78	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	75.9384	67	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457075.1	s__MED-G11 sp002457075	75.8059	53	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_902598525.1	s__MED-G11 sp902598525	75.7236	58	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.61	96.61	0.83	0.83	2	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	75.6586	77	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618245.1	s__MS024-2A sp902618245	75.6416	75	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_004321735.1	s__MED-G14 sp004321735	75.5631	57	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.77	95.40	0.78	0.75	4	-
GCA_902577515.1	s__MED-G11 sp902577515	75.4207	58	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.13	99.13	0.84	0.84	2	-
GCF_900105145.1	s__Polaribacter sp900105145	75.2695	79	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	74.925	52	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 15:03:17,244] [INFO] GTDB search result was written to OceanDNA-b7123/result_gtdb.tsv
[2023-03-14 15:03:17,244] [INFO] ===== GTDB Search completed =====
[2023-03-14 15:03:17,245] [INFO] DFAST_QC result json was written to OceanDNA-b7123/dqc_result.json
[2023-03-14 15:03:17,245] [INFO] DFAST_QC completed!
[2023-03-14 15:03:17,245] [INFO] Total running time: 0h1m21s