[2023-03-17 11:30:46,815] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:30:46,815] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:30:46,816] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference
[2023-03-17 11:30:48,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:30:48,713] [INFO] Task started: Prodigal
[2023-03-17 11:30:48,713] [INFO] Running command: cat /var/lib/cwl/stgc0e25b07-7103-4588-adaa-c114ee263cb6/OceanDNA-b23020.fa | prodigal -d OceanDNA-b23020/cds.fna -a OceanDNA-b23020/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:31:10,949] [INFO] Task succeeded: Prodigal
[2023-03-17 11:31:10,949] [INFO] Task started: HMMsearch
[2023-03-17 11:31:10,949] [INFO] Running command: hmmsearch --tblout OceanDNA-b23020/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference/reference_markers.hmm OceanDNA-b23020/protein.faa > /dev/null
[2023-03-17 11:31:11,130] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:31:11,131] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc0e25b07-7103-4588-adaa-c114ee263cb6/OceanDNA-b23020.fa]
[2023-03-17 11:31:11,159] [INFO] Query marker FASTA was written to OceanDNA-b23020/markers.fasta
[2023-03-17 11:31:11,161] [INFO] Task started: Blastn
[2023-03-17 11:31:11,161] [INFO] Running command: blastn -query OceanDNA-b23020/markers.fasta -db /var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference/reference_markers.fasta -out OceanDNA-b23020/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:31:11,675] [INFO] Task succeeded: Blastn
[2023-03-17 11:31:11,676] [INFO] Selected 15 target genomes.
[2023-03-17 11:31:11,676] [INFO] Target genome list was writen to OceanDNA-b23020/target_genomes.txt
[2023-03-17 11:31:11,690] [INFO] Task started: fastANI
[2023-03-17 11:31:11,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0e25b07-7103-4588-adaa-c114ee263cb6/OceanDNA-b23020.fa --refList OceanDNA-b23020/target_genomes.txt --output OceanDNA-b23020/fastani_result.tsv --threads 1
[2023-03-17 11:31:25,436] [INFO] Task succeeded: fastANI
[2023-03-17 11:31:25,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:31:25,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:31:25,443] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:31:25,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:31:25,443] [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	74.6751	91	895	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.6374	83	895	95	below_threshold
Frankia irregularis	strain=DSM 45899	GCA_001536285.1	795642	795642	type	True	74.6325	102	895	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	74.6282	52	895	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	74.6184	100	895	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.6165	81	895	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.6143	82	895	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	74.6129	92	895	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	74.5535	53	895	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:31:25,444] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23020/tc_result.tsv
[2023-03-17 11:31:25,444] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:31:25,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:31:25,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference/checkm_data
[2023-03-17 11:31:25,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:31:25,454] [INFO] Task started: CheckM
[2023-03-17 11:31:25,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23020/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23020/checkm_input OceanDNA-b23020/checkm_result
[2023-03-17 11:32:19,670] [INFO] Task succeeded: CheckM
[2023-03-17 11:32:19,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.24%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:32:19,696] [INFO] ===== Completeness check finished =====
[2023-03-17 11:32:19,696] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:32:19,697] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23020/markers.fasta)
[2023-03-17 11:32:19,698] [INFO] Task started: Blastn
[2023-03-17 11:32:19,698] [INFO] Running command: blastn -query OceanDNA-b23020/markers.fasta -db /var/lib/cwl/stgb9627152-aa1f-44ec-ad76-0af51d33e8e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23020/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:32:20,385] [INFO] Task succeeded: Blastn
[2023-03-17 11:32:20,386] [INFO] Selected 16 target genomes.
[2023-03-17 11:32:20,386] [INFO] Target genome list was writen to OceanDNA-b23020/target_genomes_gtdb.txt
[2023-03-17 11:32:20,448] [INFO] Task started: fastANI
[2023-03-17 11:32:20,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0e25b07-7103-4588-adaa-c114ee263cb6/OceanDNA-b23020.fa --refList OceanDNA-b23020/target_genomes_gtdb.txt --output OceanDNA-b23020/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:32:30,945] [INFO] Task succeeded: fastANI
[2023-03-17 11:32:30,952] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:32:30,953] [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_011053145.1	s__DRLC01 sp011053145	76.5715	133	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DRLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.4885	326	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.4285	188	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140785.1	s__JABFRZ01 sp013140785	76.1957	149	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	75.8357	171	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	75.8128	145	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	75.784	186	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	75.776	96	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	75.7718	174	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	75.3928	199	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	75.3553	253	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789645.1	s__SXXH01 sp005789645	75.2466	94	895	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	99.62	99.60	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-17 11:32:30,953] [INFO] GTDB search result was written to OceanDNA-b23020/result_gtdb.tsv
[2023-03-17 11:32:30,953] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:32:30,954] [INFO] DFAST_QC result json was written to OceanDNA-b23020/dqc_result.json
[2023-03-17 11:32:30,954] [INFO] DFAST_QC completed!
[2023-03-17 11:32:30,955] [INFO] Total running time: 0h1m44s