[2023-03-15 14:47:21,438] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,441] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference
[2023-03-15 14:47:22,519] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,519] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,520] [INFO] Running command: cat /var/lib/cwl/stgcd337f8f-2d7f-4aa4-97ca-2523939ec3f9/OceanDNA-b31973.fa | prodigal -d OceanDNA-b31973/cds.fna -a OceanDNA-b31973/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:34,192] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:34,192] [INFO] Task started: HMMsearch
[2023-03-15 14:47:34,193] [INFO] Running command: hmmsearch --tblout OceanDNA-b31973/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference/reference_markers.hmm OceanDNA-b31973/protein.faa > /dev/null
[2023-03-15 14:47:34,371] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:34,372] [INFO] Found 6/6 markers.
[2023-03-15 14:47:34,423] [INFO] Query marker FASTA was written to OceanDNA-b31973/markers.fasta
[2023-03-15 14:47:34,424] [INFO] Task started: Blastn
[2023-03-15 14:47:34,424] [INFO] Running command: blastn -query OceanDNA-b31973/markers.fasta -db /var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference/reference_markers.fasta -out OceanDNA-b31973/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:35,049] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:35,061] [INFO] Selected 21 target genomes.
[2023-03-15 14:47:35,062] [INFO] Target genome list was writen to OceanDNA-b31973/target_genomes.txt
[2023-03-15 14:47:35,074] [INFO] Task started: fastANI
[2023-03-15 14:47:35,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd337f8f-2d7f-4aa4-97ca-2523939ec3f9/OceanDNA-b31973.fa --refList OceanDNA-b31973/target_genomes.txt --output OceanDNA-b31973/fastani_result.tsv --threads 1
[2023-03-15 14:47:48,000] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:48,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:47:48,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:47:48,008] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:47:48,008] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:47:48,008] [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
Sphingorhabdus wooponensis	strain=03SU3-P	GCA_003933235.1	940136	940136	type	True	81.7631	415	606	95	below_threshold
Sphingorhabdus rigui	strain=DSM 29050	GCA_014196595.1	1282858	1282858	type	True	80.5112	379	606	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	78.3173	219	606	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	78.2876	250	606	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	77.7751	229	606	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	77.266	138	606	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	76.336	51	606	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	75.9175	59	606	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	75.8225	50	606	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	75.7952	50	606	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:47:48,013] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31973/tc_result.tsv
[2023-03-15 14:47:48,022] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:47:48,022] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:47:48,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference/checkm_data
[2023-03-15 14:47:48,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:47:48,061] [INFO] Task started: CheckM
[2023-03-15 14:47:48,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31973/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31973/checkm_input OceanDNA-b31973/checkm_result
[2023-03-15 14:48:21,126] [INFO] Task succeeded: CheckM
[2023-03-15 14:48:21,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 14:48:21,232] [INFO] ===== Completeness check finished =====
[2023-03-15 14:48:21,232] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:48:21,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31973/markers.fasta)
[2023-03-15 14:48:21,234] [INFO] Task started: Blastn
[2023-03-15 14:48:21,234] [INFO] Running command: blastn -query OceanDNA-b31973/markers.fasta -db /var/lib/cwl/stg46c849b0-77aa-4fa0-991a-f86493991d71/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31973/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:48:22,337] [INFO] Task succeeded: Blastn
[2023-03-15 14:48:22,346] [INFO] Selected 10 target genomes.
[2023-03-15 14:48:22,346] [INFO] Target genome list was writen to OceanDNA-b31973/target_genomes_gtdb.txt
[2023-03-15 14:48:22,406] [INFO] Task started: fastANI
[2023-03-15 14:48:22,406] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd337f8f-2d7f-4aa4-97ca-2523939ec3f9/OceanDNA-b31973.fa --refList OceanDNA-b31973/target_genomes_gtdb.txt --output OceanDNA-b31973/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:48:27,107] [INFO] Task succeeded: fastANI
[2023-03-15 14:48:27,113] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:48:27,113] [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_903821685.1	s__Sphingorhabdus_B sp903821685	94.1542	456	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.60	99.60	0.86	0.86	2	-
GCA_002278855.1	s__Sphingorhabdus_B sp002278855	85.9847	473	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.65	99.65	0.97	0.97	2	-
GCA_016462305.1	s__Sphingorhabdus_B sp016462305	82.1653	331	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.63	98.63	0.82	0.82	2	-
GCF_003933235.1	s__Sphingorhabdus_B wooponensis	81.763	415	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868245.1	s__Sphingorhabdus_B sp903868245	81.4796	358	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299895.1	s__Sphingorhabdus_B sp002299895	81.2371	378	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282385.1	s__Sphingorhabdus_B sp002282385	80.7243	359	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.98	99.95	0.99	0.98	4	-
GCF_014196595.1	s__Sphingorhabdus_B rigui	80.5112	379	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299195.1	s__Sphingorhabdus_B sp002299195	80.029	303	606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:48:27,117] [INFO] GTDB search result was written to OceanDNA-b31973/result_gtdb.tsv
[2023-03-15 14:48:27,122] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:48:27,127] [INFO] DFAST_QC result json was written to OceanDNA-b31973/dqc_result.json
[2023-03-15 14:48:27,127] [INFO] DFAST_QC completed!
[2023-03-15 14:48:27,127] [INFO] Total running time: 0h1m6s