[2023-03-19 02:16:59,692] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,694] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference
[2023-03-19 02:17:00,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,809] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,810] [INFO] Running command: cat /var/lib/cwl/stg3e9938c6-fd4e-4259-8ed9-3bc5c007806f/OceanDNA-b22322.fa | prodigal -d OceanDNA-b22322/cds.fna -a OceanDNA-b22322/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:32,571] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:32,571] [INFO] Task started: HMMsearch
[2023-03-19 02:17:32,571] [INFO] Running command: hmmsearch --tblout OceanDNA-b22322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference/reference_markers.hmm OceanDNA-b22322/protein.faa > /dev/null
[2023-03-19 02:17:32,824] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:32,825] [INFO] Found 6/6 markers.
[2023-03-19 02:17:32,860] [INFO] Query marker FASTA was written to OceanDNA-b22322/markers.fasta
[2023-03-19 02:17:32,861] [INFO] Task started: Blastn
[2023-03-19 02:17:32,862] [INFO] Running command: blastn -query OceanDNA-b22322/markers.fasta -db /var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference/reference_markers.fasta -out OceanDNA-b22322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:33,379] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:33,380] [INFO] Selected 28 target genomes.
[2023-03-19 02:17:33,380] [INFO] Target genome list was writen to OceanDNA-b22322/target_genomes.txt
[2023-03-19 02:17:33,394] [INFO] Task started: fastANI
[2023-03-19 02:17:33,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e9938c6-fd4e-4259-8ed9-3bc5c007806f/OceanDNA-b22322.fa --refList OceanDNA-b22322/target_genomes.txt --output OceanDNA-b22322/fastani_result.tsv --threads 1
[2023-03-19 02:17:56,476] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:56,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:17:56,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:17:56,482] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:17:56,482] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:17:56,482] [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
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.6386	54	1702	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.5709	71	1702	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.4403	72	1702	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.4303	69	1702	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.4281	60	1702	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:17:56,841] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22322/tc_result.tsv
[2023-03-19 02:17:56,842] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:17:56,842] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:17:56,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference/checkm_data
[2023-03-19 02:17:56,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:17:56,942] [INFO] Task started: CheckM
[2023-03-19 02:17:56,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22322/checkm_input OceanDNA-b22322/checkm_result
[2023-03-19 02:19:14,475] [INFO] Task succeeded: CheckM
[2023-03-19 02:19:14,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:19:14,479] [INFO] ===== Completeness check finished =====
[2023-03-19 02:19:14,479] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:19:14,479] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22322/markers.fasta)
[2023-03-19 02:19:14,480] [INFO] Task started: Blastn
[2023-03-19 02:19:14,481] [INFO] Running command: blastn -query OceanDNA-b22322/markers.fasta -db /var/lib/cwl/stg9274761f-6147-425b-9c82-d43568cd2fe7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:19:15,189] [INFO] Task succeeded: Blastn
[2023-03-19 02:19:15,190] [INFO] Selected 32 target genomes.
[2023-03-19 02:19:15,190] [INFO] Target genome list was writen to OceanDNA-b22322/target_genomes_gtdb.txt
[2023-03-19 02:19:15,221] [INFO] Task started: fastANI
[2023-03-19 02:19:15,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e9938c6-fd4e-4259-8ed9-3bc5c007806f/OceanDNA-b22322.fa --refList OceanDNA-b22322/target_genomes_gtdb.txt --output OceanDNA-b22322/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:19:40,310] [INFO] Task succeeded: fastANI
[2023-03-19 02:19:40,315] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:19:40,315] [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_003576855.1	s__Lacipirellula sp003576855	75.7676	57	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003389215.1	s__MB-PLM-2 sp003389215	75.7505	91	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__MB-PLM-2	95.0	99.69	99.49	0.94	0.93	4	-
GCA_012719125.1	s__JAAYAY01 sp012719125	75.7038	56	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYAY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	75.6386	54	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.5709	71	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793185.1	s__JAEUIK01 sp016793185	75.5255	54	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JAEUIK01;g__JAEUIK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728855.1	s__JABWBD01 sp012728855	75.225	56	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822735.1	s__PNKZ01 sp013822735	75.1066	51	1702	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__PNKZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:19:40,316] [INFO] GTDB search result was written to OceanDNA-b22322/result_gtdb.tsv
[2023-03-19 02:19:40,316] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:19:40,317] [INFO] DFAST_QC result json was written to OceanDNA-b22322/dqc_result.json
[2023-03-19 02:19:40,317] [INFO] DFAST_QC completed!
[2023-03-19 02:19:40,317] [INFO] Total running time: 0h2m41s