[2023-03-16 07:34:40,566] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,566] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference
[2023-03-16 07:34:42,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,228] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,228] [INFO] Running command: cat /var/lib/cwl/stg9dee0091-a523-4547-a8dd-9d0592056215/OceanDNA-b22093.fa | prodigal -d OceanDNA-b22093/cds.fna -a OceanDNA-b22093/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:35:07,814] [INFO] Task succeeded: Prodigal
[2023-03-16 07:35:07,814] [INFO] Task started: HMMsearch
[2023-03-16 07:35:07,814] [INFO] Running command: hmmsearch --tblout OceanDNA-b22093/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference/reference_markers.hmm OceanDNA-b22093/protein.faa > /dev/null
[2023-03-16 07:35:08,024] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:35:08,024] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9dee0091-a523-4547-a8dd-9d0592056215/OceanDNA-b22093.fa]
[2023-03-16 07:35:08,049] [INFO] Query marker FASTA was written to OceanDNA-b22093/markers.fasta
[2023-03-16 07:35:08,050] [INFO] Task started: Blastn
[2023-03-16 07:35:08,050] [INFO] Running command: blastn -query OceanDNA-b22093/markers.fasta -db /var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference/reference_markers.fasta -out OceanDNA-b22093/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:08,680] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:08,681] [INFO] Selected 9 target genomes.
[2023-03-16 07:35:08,681] [INFO] Target genome list was writen to OceanDNA-b22093/target_genomes.txt
[2023-03-16 07:35:08,688] [INFO] Task started: fastANI
[2023-03-16 07:35:08,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dee0091-a523-4547-a8dd-9d0592056215/OceanDNA-b22093.fa --refList OceanDNA-b22093/target_genomes.txt --output OceanDNA-b22093/fastani_result.tsv --threads 1
[2023-03-16 07:35:16,334] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:16,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:16,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:16,341] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:16,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:35:16,341] [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
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	82.1227	599	901	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	82.0028	609	901	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.8345	150	901	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.758	76	901	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.3779	73	901	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.8325	192	901	95	below_threshold
Burkholderia pseudomultivorans		GCA_902499075.1	1207504	1207504	suspected-type	True	74.8215	79	901	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	74.5277	64	901	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:35:16,342] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22093/tc_result.tsv
[2023-03-16 07:35:16,344] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:16,344] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:16,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference/checkm_data
[2023-03-16 07:35:16,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:16,351] [INFO] Task started: CheckM
[2023-03-16 07:35:16,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22093/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22093/checkm_input OceanDNA-b22093/checkm_result
[2023-03-16 07:36:17,538] [INFO] Task succeeded: CheckM
[2023-03-16 07:36:17,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.65%
Contamintation: 4.92%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 07:36:17,550] [INFO] ===== Completeness check finished =====
[2023-03-16 07:36:17,550] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:36:17,550] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22093/markers.fasta)
[2023-03-16 07:36:17,551] [INFO] Task started: Blastn
[2023-03-16 07:36:17,551] [INFO] Running command: blastn -query OceanDNA-b22093/markers.fasta -db /var/lib/cwl/stg6ca308ff-2918-4f7a-a6e8-29fc1f19b4b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22093/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:36:18,626] [INFO] Task succeeded: Blastn
[2023-03-16 07:36:18,627] [INFO] Selected 19 target genomes.
[2023-03-16 07:36:18,627] [INFO] Target genome list was writen to OceanDNA-b22093/target_genomes_gtdb.txt
[2023-03-16 07:36:19,373] [INFO] Task started: fastANI
[2023-03-16 07:36:19,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dee0091-a523-4547-a8dd-9d0592056215/OceanDNA-b22093.fa --refList OceanDNA-b22093/target_genomes_gtdb.txt --output OceanDNA-b22093/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:31,148] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:31,155] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:36:31,156] [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_000284115.1	s__Phycisphaera mikurensis	82.0842	602	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014207595.1	s__Algisphaera agarilytica	76.8359	150	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007748075.1	s__Pan265 sp007748075	75.7757	75	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Pan265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551485.1	s__B1Sed10-187 sp003551485	75.6368	89	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__B1Sed10-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686995.1	s__GCA-2686995 sp002686995	75.4001	85	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696725.1	s__J020 sp003696725	75.3852	100	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125215.1	s__RI-382 sp016125215	75.3454	65	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__RI-382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742075.1	s__JACVCL01 sp016742075	75.201	99	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873295.1	s__VGXM01 sp016873295	75.1235	104	901	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__VGXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212795.1	s__JACRDT01 sp016212795	74.7816	66	901	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__UBA1565;f__UBA9628;g__JACRDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881505.1	s__JADGQW01 sp017881505	74.7759	68	901	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__JACORV01;g__JADGQW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:31,156] [INFO] GTDB search result was written to OceanDNA-b22093/result_gtdb.tsv
[2023-03-16 07:36:31,156] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:31,157] [INFO] DFAST_QC result json was written to OceanDNA-b22093/dqc_result.json
[2023-03-16 07:36:31,157] [INFO] DFAST_QC completed!
[2023-03-16 07:36:31,157] [INFO] Total running time: 0h1m51s