[2023-03-17 14:23:21,331] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:23:21,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:23:21,331] [INFO] DQC Reference Directory: /var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference
[2023-03-17 14:23:23,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:23:23,907] [INFO] Task started: Prodigal
[2023-03-17 14:23:23,907] [INFO] Running command: cat /var/lib/cwl/stgbdfe8218-497b-40f9-b1c0-d42c932cf9f3/OceanDNA-b43418.fa | prodigal -d OceanDNA-b43418/cds.fna -a OceanDNA-b43418/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:23:30,976] [INFO] Task succeeded: Prodigal
[2023-03-17 14:23:30,977] [INFO] Task started: HMMsearch
[2023-03-17 14:23:30,977] [INFO] Running command: hmmsearch --tblout OceanDNA-b43418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference/reference_markers.hmm OceanDNA-b43418/protein.faa > /dev/null
[2023-03-17 14:23:31,197] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:23:31,198] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbdfe8218-497b-40f9-b1c0-d42c932cf9f3/OceanDNA-b43418.fa]
[2023-03-17 14:23:31,211] [INFO] Query marker FASTA was written to OceanDNA-b43418/markers.fasta
[2023-03-17 14:23:31,211] [INFO] Task started: Blastn
[2023-03-17 14:23:31,211] [INFO] Running command: blastn -query OceanDNA-b43418/markers.fasta -db /var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference/reference_markers.fasta -out OceanDNA-b43418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:23:31,871] [INFO] Task succeeded: Blastn
[2023-03-17 14:23:31,872] [INFO] Selected 25 target genomes.
[2023-03-17 14:23:31,872] [INFO] Target genome list was writen to OceanDNA-b43418/target_genomes.txt
[2023-03-17 14:23:31,888] [INFO] Task started: fastANI
[2023-03-17 14:23:31,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdfe8218-497b-40f9-b1c0-d42c932cf9f3/OceanDNA-b43418.fa --refList OceanDNA-b43418/target_genomes.txt --output OceanDNA-b43418/fastani_result.tsv --threads 1
[2023-03-17 14:23:46,228] [INFO] Task succeeded: fastANI
[2023-03-17 14:23:46,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:23:46,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:23:46,232] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:23:46,233] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:23:46,233] [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
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	77.8122	71	398	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	77.6729	88	398	95	below_threshold
Thiomicrorhabdus arctica	strain=DSM 13458	GCA_000381085.1	131540	131540	type	True	77.3277	55	398	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:23:46,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43418/tc_result.tsv
[2023-03-17 14:23:46,233] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:23:46,233] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:23:46,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference/checkm_data
[2023-03-17 14:23:46,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:23:46,237] [INFO] Task started: CheckM
[2023-03-17 14:23:46,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43418/checkm_input OceanDNA-b43418/checkm_result
[2023-03-17 14:24:13,369] [INFO] Task succeeded: CheckM
[2023-03-17 14:24:13,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 14:24:13,371] [INFO] ===== Completeness check finished =====
[2023-03-17 14:24:13,371] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:24:13,371] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43418/markers.fasta)
[2023-03-17 14:24:13,371] [INFO] Task started: Blastn
[2023-03-17 14:24:13,371] [INFO] Running command: blastn -query OceanDNA-b43418/markers.fasta -db /var/lib/cwl/stga715cbec-fa77-4be1-9756-0aeb5e710f02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:24:14,154] [INFO] Task succeeded: Blastn
[2023-03-17 14:24:14,155] [INFO] Selected 20 target genomes.
[2023-03-17 14:24:14,155] [INFO] Target genome list was writen to OceanDNA-b43418/target_genomes_gtdb.txt
[2023-03-17 14:24:14,215] [INFO] Task started: fastANI
[2023-03-17 14:24:14,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdfe8218-497b-40f9-b1c0-d42c932cf9f3/OceanDNA-b43418.fa --refList OceanDNA-b43418/target_genomes_gtdb.txt --output OceanDNA-b43418/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:24:23,092] [INFO] Task succeeded: fastANI
[2023-03-17 14:24:23,096] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 14:24:23,096] [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_005885815.1	s__Thiomicrorhabdus sediminis	77.8122	71	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702325.1	s__Thiomicrorhabdus sp000702325	77.6771	93	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478585.1	s__Thiomicrorhabdus sp000478585	77.6267	117	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299245.1	s__Thiomicrorhabdus sp002299245	77.5905	51	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.68	99.68	0.83	0.83	2	-
GCF_000381085.1	s__Thiomicrorhabdus arctica	77.3277	55	398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:24:23,096] [INFO] GTDB search result was written to OceanDNA-b43418/result_gtdb.tsv
[2023-03-17 14:24:23,096] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:24:23,097] [INFO] DFAST_QC result json was written to OceanDNA-b43418/dqc_result.json
[2023-03-17 14:24:23,097] [INFO] DFAST_QC completed!
[2023-03-17 14:24:23,097] [INFO] Total running time: 0h1m2s