[2023-03-16 06:35:45,607] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:35:45,608] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:35:45,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference
[2023-03-16 06:35:46,692] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:35:46,693] [INFO] Task started: Prodigal
[2023-03-16 06:35:46,693] [INFO] Running command: cat /var/lib/cwl/stgf040487c-9b8e-44c1-bd84-8816e2021028/OceanDNA-b1753.fa | prodigal -d OceanDNA-b1753/cds.fna -a OceanDNA-b1753/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:35:58,627] [INFO] Task succeeded: Prodigal
[2023-03-16 06:35:58,627] [INFO] Task started: HMMsearch
[2023-03-16 06:35:58,627] [INFO] Running command: hmmsearch --tblout OceanDNA-b1753/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference/reference_markers.hmm OceanDNA-b1753/protein.faa > /dev/null
[2023-03-16 06:35:58,972] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:35:58,973] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf040487c-9b8e-44c1-bd84-8816e2021028/OceanDNA-b1753.fa]
[2023-03-16 06:35:58,991] [INFO] Query marker FASTA was written to OceanDNA-b1753/markers.fasta
[2023-03-16 06:35:58,993] [INFO] Task started: Blastn
[2023-03-16 06:35:58,993] [INFO] Running command: blastn -query OceanDNA-b1753/markers.fasta -db /var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference/reference_markers.fasta -out OceanDNA-b1753/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:36:02,554] [INFO] Task succeeded: Blastn
[2023-03-16 06:36:02,555] [INFO] Selected 29 target genomes.
[2023-03-16 06:36:02,555] [INFO] Target genome list was writen to OceanDNA-b1753/target_genomes.txt
[2023-03-16 06:36:02,572] [INFO] Task started: fastANI
[2023-03-16 06:36:02,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgf040487c-9b8e-44c1-bd84-8816e2021028/OceanDNA-b1753.fa --refList OceanDNA-b1753/target_genomes.txt --output OceanDNA-b1753/fastani_result.tsv --threads 1
[2023-03-16 06:36:23,672] [INFO] Task succeeded: fastANI
[2023-03-16 06:36:23,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:36:23,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:36:23,678] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:36:23,678] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:36:23,678] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.3204	69	570	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.9595	69	570	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.8549	78	570	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.7084	68	570	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.6855	54	570	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.4609	52	570	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:36:23,679] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1753/tc_result.tsv
[2023-03-16 06:36:23,679] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:36:23,679] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:36:23,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference/checkm_data
[2023-03-16 06:36:23,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:36:23,694] [INFO] Task started: CheckM
[2023-03-16 06:36:23,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1753/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1753/checkm_input OceanDNA-b1753/checkm_result
[2023-03-16 06:36:58,621] [INFO] Task succeeded: CheckM
[2023-03-16 06:36:58,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:36:58,624] [INFO] ===== Completeness check finished =====
[2023-03-16 06:36:58,625] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:36:58,625] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1753/markers.fasta)
[2023-03-16 06:36:58,626] [INFO] Task started: Blastn
[2023-03-16 06:36:58,626] [INFO] Running command: blastn -query OceanDNA-b1753/markers.fasta -db /var/lib/cwl/stgf47488d8-be1f-4375-8a50-187997c6ba6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1753/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:36:59,890] [INFO] Task succeeded: Blastn
[2023-03-16 06:36:59,892] [INFO] Selected 15 target genomes.
[2023-03-16 06:36:59,892] [INFO] Target genome list was writen to OceanDNA-b1753/target_genomes_gtdb.txt
[2023-03-16 06:36:59,919] [INFO] Task started: fastANI
[2023-03-16 06:36:59,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgf040487c-9b8e-44c1-bd84-8816e2021028/OceanDNA-b1753.fa --refList OceanDNA-b1753/target_genomes_gtdb.txt --output OceanDNA-b1753/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:37:07,716] [INFO] Task succeeded: fastANI
[2023-03-16 06:37:07,722] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:37:07,722] [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_002694825.1	s__UBA11606 sp002694825	79.4966	295	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_002699625.1	s__UBA11606 sp002699625	79.1326	242	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	79.1164	263	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_905480195.1	s__UBA11606 sp905480195	77.7203	192	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845585.1	s__UBA11606 sp016845585	77.5917	179	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937405.1	s__UBA11606 sp009937405	76.4838	83	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCA_009842325.1	s__VYCW01 sp009842325	76.3803	79	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.89	99.81	0.98	0.97	3	-
GCA_016649895.1	s__Actinomarinicola sp016649895	76.1077	65	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:37:07,722] [INFO] GTDB search result was written to OceanDNA-b1753/result_gtdb.tsv
[2023-03-16 06:37:07,723] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:37:07,724] [INFO] DFAST_QC result json was written to OceanDNA-b1753/dqc_result.json
[2023-03-16 06:37:07,725] [INFO] DFAST_QC completed!
[2023-03-16 06:37:07,725] [INFO] Total running time: 0h1m22s