[2023-03-19 02:05:11,584] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,584] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference
[2023-03-19 02:05:13,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,261] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,261] [INFO] Running command: cat /var/lib/cwl/stg4efe85e0-7414-443d-b90d-507e40465954/OceanDNA-b22460.fa | prodigal -d OceanDNA-b22460/cds.fna -a OceanDNA-b22460/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:54,509] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:54,509] [INFO] Task started: HMMsearch
[2023-03-19 02:05:54,509] [INFO] Running command: hmmsearch --tblout OceanDNA-b22460/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference/reference_markers.hmm OceanDNA-b22460/protein.faa > /dev/null
[2023-03-19 02:05:54,787] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:54,788] [INFO] Found 6/6 markers.
[2023-03-19 02:05:54,824] [INFO] Query marker FASTA was written to OceanDNA-b22460/markers.fasta
[2023-03-19 02:05:54,825] [INFO] Task started: Blastn
[2023-03-19 02:05:54,825] [INFO] Running command: blastn -query OceanDNA-b22460/markers.fasta -db /var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference/reference_markers.fasta -out OceanDNA-b22460/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:55,377] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:55,378] [INFO] Selected 17 target genomes.
[2023-03-19 02:05:55,378] [INFO] Target genome list was writen to OceanDNA-b22460/target_genomes.txt
[2023-03-19 02:05:55,415] [INFO] Task started: fastANI
[2023-03-19 02:05:55,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efe85e0-7414-443d-b90d-507e40465954/OceanDNA-b22460.fa --refList OceanDNA-b22460/target_genomes.txt --output OceanDNA-b22460/fastani_result.tsv --threads 1
[2023-03-19 02:06:13,729] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:13,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:06:13,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:06:13,736] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:06:13,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:06:13,736] [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
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	78.7648	658	2103	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.2117	305	2103	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.1822	325	2103	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	76.8262	271	2103	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	76.5322	140	2103	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.4712	234	2103	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	76.4568	161	2103	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.3599	146	2103	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	76.0218	69	2103	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:06:13,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22460/tc_result.tsv
[2023-03-19 02:06:13,737] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:06:13,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:06:13,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference/checkm_data
[2023-03-19 02:06:13,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:06:13,745] [INFO] Task started: CheckM
[2023-03-19 02:06:13,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22460/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22460/checkm_input OceanDNA-b22460/checkm_result
[2023-03-19 02:07:53,045] [INFO] Task succeeded: CheckM
[2023-03-19 02:07:53,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:07:53,272] [INFO] ===== Completeness check finished =====
[2023-03-19 02:07:53,272] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:07:53,272] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22460/markers.fasta)
[2023-03-19 02:07:53,277] [INFO] Task started: Blastn
[2023-03-19 02:07:53,277] [INFO] Running command: blastn -query OceanDNA-b22460/markers.fasta -db /var/lib/cwl/stg6e9d41ef-6d87-4df8-8080-f20bd0a92230/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22460/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:07:53,992] [INFO] Task succeeded: Blastn
[2023-03-19 02:07:54,077] [INFO] Selected 22 target genomes.
[2023-03-19 02:07:54,077] [INFO] Target genome list was writen to OceanDNA-b22460/target_genomes_gtdb.txt
[2023-03-19 02:07:54,333] [INFO] Task started: fastANI
[2023-03-19 02:07:54,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efe85e0-7414-443d-b90d-507e40465954/OceanDNA-b22460.fa --refList OceanDNA-b22460/target_genomes_gtdb.txt --output OceanDNA-b22460/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:08:15,467] [INFO] Task succeeded: fastANI
[2023-03-19 02:08:15,474] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:08:15,474] [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_007860105.1	s__Rhodopirellula sp007860105	98.5844	1959	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859855.1	s__Rhodopirellula solitaria	78.7815	655	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	77.2025	306	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCA_007745635.1	s__Stieleria sp002167455	76.8716	55	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	98.72	98.72	0.91	0.91	2	-
GCF_000346505.1	s__Rhodopirellula sallentina	76.8353	270	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	76.5473	139	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	76.4712	234	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	76.4568	161	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.3467	147	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCA_007859835.1	s__Novipirellula sp007859835	76.0749	78	2103	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:08:15,474] [INFO] GTDB search result was written to OceanDNA-b22460/result_gtdb.tsv
[2023-03-19 02:08:15,474] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:08:15,476] [INFO] DFAST_QC result json was written to OceanDNA-b22460/dqc_result.json
[2023-03-19 02:08:15,476] [INFO] DFAST_QC completed!
[2023-03-19 02:08:15,476] [INFO] Total running time: 0h3m4s