[2023-03-16 07:09:52,127] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:09:52,127] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:09:52,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference
[2023-03-16 07:09:56,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:09:56,341] [INFO] Task started: Prodigal
[2023-03-16 07:09:56,341] [INFO] Running command: cat /var/lib/cwl/stge6792a59-d049-4b70-9ddb-11986b646603/OceanDNA-b519.fa | prodigal -d OceanDNA-b519/cds.fna -a OceanDNA-b519/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:10:09,046] [INFO] Task succeeded: Prodigal
[2023-03-16 07:10:09,047] [INFO] Task started: HMMsearch
[2023-03-16 07:10:09,047] [INFO] Running command: hmmsearch --tblout OceanDNA-b519/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference/reference_markers.hmm OceanDNA-b519/protein.faa > /dev/null
[2023-03-16 07:10:09,305] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:10:09,305] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge6792a59-d049-4b70-9ddb-11986b646603/OceanDNA-b519.fa]
[2023-03-16 07:10:09,323] [INFO] Query marker FASTA was written to OceanDNA-b519/markers.fasta
[2023-03-16 07:10:09,325] [INFO] Task started: Blastn
[2023-03-16 07:10:09,325] [INFO] Running command: blastn -query OceanDNA-b519/markers.fasta -db /var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference/reference_markers.fasta -out OceanDNA-b519/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:10:14,283] [INFO] Task succeeded: Blastn
[2023-03-16 07:10:14,285] [INFO] Selected 11 target genomes.
[2023-03-16 07:10:14,285] [INFO] Target genome list was writen to OceanDNA-b519/target_genomes.txt
[2023-03-16 07:10:14,325] [INFO] Task started: fastANI
[2023-03-16 07:10:14,325] [INFO] Running command: fastANI --query /var/lib/cwl/stge6792a59-d049-4b70-9ddb-11986b646603/OceanDNA-b519.fa --refList OceanDNA-b519/target_genomes.txt --output OceanDNA-b519/fastani_result.tsv --threads 1
[2023-03-16 07:10:24,022] [INFO] Task succeeded: fastANI
[2023-03-16 07:10:24,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:10:24,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:10:24,076] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:10:24,076] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:10:24,076] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	79.951	413	676	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.7318	180	676	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.4073	229	676	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.0892	238	676	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.4822	140	676	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.3341	122	676	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	75.2921	95	676	95	below_threshold
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	75.1798	92	676	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	75.1514	96	676	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	75.1423	97	676	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:10:24,077] [INFO] DFAST Taxonomy check result was written to OceanDNA-b519/tc_result.tsv
[2023-03-16 07:10:24,077] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:10:24,077] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:10:24,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference/checkm_data
[2023-03-16 07:10:24,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:10:24,393] [INFO] Task started: CheckM
[2023-03-16 07:10:24,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b519/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b519/checkm_input OceanDNA-b519/checkm_result
[2023-03-16 07:11:11,833] [INFO] Task succeeded: CheckM
[2023-03-16 07:11:11,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:11:11,839] [INFO] ===== Completeness check finished =====
[2023-03-16 07:11:11,839] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:11:11,839] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b519/markers.fasta)
[2023-03-16 07:11:11,840] [INFO] Task started: Blastn
[2023-03-16 07:11:11,840] [INFO] Running command: blastn -query OceanDNA-b519/markers.fasta -db /var/lib/cwl/stgc71c9604-c30e-4136-b289-aff0f8e98371/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b519/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:11:13,057] [INFO] Task succeeded: Blastn
[2023-03-16 07:11:13,060] [INFO] Selected 8 target genomes.
[2023-03-16 07:11:13,060] [INFO] Target genome list was writen to OceanDNA-b519/target_genomes_gtdb.txt
[2023-03-16 07:11:13,066] [INFO] Task started: fastANI
[2023-03-16 07:11:13,066] [INFO] Running command: fastANI --query /var/lib/cwl/stge6792a59-d049-4b70-9ddb-11986b646603/OceanDNA-b519.fa --refList OceanDNA-b519/target_genomes_gtdb.txt --output OceanDNA-b519/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:11:18,817] [INFO] Task succeeded: fastANI
[2023-03-16 07:11:18,822] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:11:18,822] [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_004364865.1	s__Ilumatobacter fluminis	79.9377	414	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	79.4535	300	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	78.0899	221	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_007693335.1	s__SKSP01 sp007693335	77.9652	213	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.7131	181	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.562	215	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.4082	228	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	77.1	237	676	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:11:18,824] [INFO] GTDB search result was written to OceanDNA-b519/result_gtdb.tsv
[2023-03-16 07:11:18,825] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:11:18,827] [INFO] DFAST_QC result json was written to OceanDNA-b519/dqc_result.json
[2023-03-16 07:11:18,827] [INFO] DFAST_QC completed!
[2023-03-16 07:11:18,827] [INFO] Total running time: 0h1m27s