[2023-03-17 13:01:51,411] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,411] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,411] [INFO] DQC Reference Directory: /var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference
[2023-03-17 13:01:52,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,651] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,651] [INFO] Running command: cat /var/lib/cwl/stgaf17acb5-9e14-4412-a33b-eaf622da516e/OceanDNA-b27535.fa | prodigal -d OceanDNA-b27535/cds.fna -a OceanDNA-b27535/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:05,471] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:05,471] [INFO] Task started: HMMsearch
[2023-03-17 13:02:05,471] [INFO] Running command: hmmsearch --tblout OceanDNA-b27535/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference/reference_markers.hmm OceanDNA-b27535/protein.faa > /dev/null
[2023-03-17 13:02:05,706] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:05,707] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaf17acb5-9e14-4412-a33b-eaf622da516e/OceanDNA-b27535.fa]
[2023-03-17 13:02:05,730] [INFO] Query marker FASTA was written to OceanDNA-b27535/markers.fasta
[2023-03-17 13:02:05,730] [INFO] Task started: Blastn
[2023-03-17 13:02:05,730] [INFO] Running command: blastn -query OceanDNA-b27535/markers.fasta -db /var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference/reference_markers.fasta -out OceanDNA-b27535/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:06,270] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:06,271] [INFO] Selected 15 target genomes.
[2023-03-17 13:02:06,271] [INFO] Target genome list was writen to OceanDNA-b27535/target_genomes.txt
[2023-03-17 13:02:06,279] [INFO] Task started: fastANI
[2023-03-17 13:02:06,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf17acb5-9e14-4412-a33b-eaf622da516e/OceanDNA-b27535.fa --refList OceanDNA-b27535/target_genomes.txt --output OceanDNA-b27535/fastani_result.tsv --threads 1
[2023-03-17 13:02:15,934] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:15,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:15,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:15,941] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:15,941] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:02:15,942] [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
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.1837	66	601	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	76.0271	80	601	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.0191	98	601	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	75.7041	66	601	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	75.7032	59	601	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	75.6756	55	601	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	75.6383	70	601	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	75.6383	70	601	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.6383	70	601	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	75.6104	67	601	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:02:15,942] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27535/tc_result.tsv
[2023-03-17 13:02:15,942] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:15,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:15,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference/checkm_data
[2023-03-17 13:02:15,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:15,948] [INFO] Task started: CheckM
[2023-03-17 13:02:15,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27535/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27535/checkm_input OceanDNA-b27535/checkm_result
[2023-03-17 13:02:51,758] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:51,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:51,761] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:51,761] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:51,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27535/markers.fasta)
[2023-03-17 13:02:51,762] [INFO] Task started: Blastn
[2023-03-17 13:02:51,762] [INFO] Running command: blastn -query OceanDNA-b27535/markers.fasta -db /var/lib/cwl/stgec10b260-8f89-408b-9c4b-0b49bd6afa69/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27535/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:52,438] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:52,439] [INFO] Selected 15 target genomes.
[2023-03-17 13:02:52,439] [INFO] Target genome list was writen to OceanDNA-b27535/target_genomes_gtdb.txt
[2023-03-17 13:02:52,559] [INFO] Task started: fastANI
[2023-03-17 13:02:52,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf17acb5-9e14-4412-a33b-eaf622da516e/OceanDNA-b27535.fa --refList OceanDNA-b27535/target_genomes_gtdb.txt --output OceanDNA-b27535/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:02,039] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:02,046] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:03:02,046] [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_900107235.1	s__Citreimonas salinaria	76.3855	53	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	76.1648	72	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.1416	76	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	76.093	53	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	75.8256	70	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	75.8061	91	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	75.7509	60	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	75.7208	65	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	75.6913	64	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_013093415.1	s__Halovulum dunhuangense	75.6092	67	601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:02,046] [INFO] GTDB search result was written to OceanDNA-b27535/result_gtdb.tsv
[2023-03-17 13:03:02,047] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:02,048] [INFO] DFAST_QC result json was written to OceanDNA-b27535/dqc_result.json
[2023-03-17 13:03:02,048] [INFO] DFAST_QC completed!
[2023-03-17 13:03:02,048] [INFO] Total running time: 0h1m11s