[2023-03-16 23:35:12,966] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference
[2023-03-16 23:35:14,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stgeb1dc3ba-273d-4659-9072-2f423f0dafd8/OceanDNA-a2981.fa | prodigal -d OceanDNA-a2981/cds.fna -a OceanDNA-a2981/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:21,177] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:21,178] [INFO] Task started: HMMsearch
[2023-03-16 23:35:21,178] [INFO] Running command: hmmsearch --tblout OceanDNA-a2981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference/reference_markers.hmm OceanDNA-a2981/protein.faa > /dev/null
[2023-03-16 23:35:21,320] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:21,321] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgeb1dc3ba-273d-4659-9072-2f423f0dafd8/OceanDNA-a2981.fa]
[2023-03-16 23:35:21,331] [INFO] Query marker FASTA was written to OceanDNA-a2981/markers.fasta
[2023-03-16 23:35:21,331] [INFO] Task started: Blastn
[2023-03-16 23:35:21,332] [INFO] Running command: blastn -query OceanDNA-a2981/markers.fasta -db /var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference/reference_markers.fasta -out OceanDNA-a2981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:21,777] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:21,778] [INFO] Selected 5 target genomes.
[2023-03-16 23:35:21,778] [INFO] Target genome list was writen to OceanDNA-a2981/target_genomes.txt
[2023-03-16 23:35:21,781] [INFO] Task started: fastANI
[2023-03-16 23:35:21,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1dc3ba-273d-4659-9072-2f423f0dafd8/OceanDNA-a2981.fa --refList OceanDNA-a2981/target_genomes.txt --output OceanDNA-a2981/fastani_result.tsv --threads 1
[2023-03-16 23:35:26,393] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:26,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:26,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:26,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:26,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:26,394] [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
--------------------------------------------------------------------------------
[2023-03-16 23:35:26,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2981/tc_result.tsv
[2023-03-16 23:35:26,394] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:26,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:26,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference/checkm_data
[2023-03-16 23:35:26,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:26,400] [INFO] Task started: CheckM
[2023-03-16 23:35:26,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2981/checkm_input OceanDNA-a2981/checkm_result
[2023-03-16 23:35:49,941] [INFO] Task succeeded: CheckM
[2023-03-16 23:35:49,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:35:49,943] [INFO] ===== Completeness check finished =====
[2023-03-16 23:35:49,943] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:35:49,944] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2981/markers.fasta)
[2023-03-16 23:35:49,944] [INFO] Task started: Blastn
[2023-03-16 23:35:49,944] [INFO] Running command: blastn -query OceanDNA-a2981/markers.fasta -db /var/lib/cwl/stg66a944a2-3da9-458e-8c84-3efb6a0d5946/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:50,468] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:50,469] [INFO] Selected 8 target genomes.
[2023-03-16 23:35:50,469] [INFO] Target genome list was writen to OceanDNA-a2981/target_genomes_gtdb.txt
[2023-03-16 23:35:50,562] [INFO] Task started: fastANI
[2023-03-16 23:35:50,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1dc3ba-273d-4659-9072-2f423f0dafd8/OceanDNA-a2981.fa --refList OceanDNA-a2981/target_genomes_gtdb.txt --output OceanDNA-a2981/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:35:52,923] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:52,929] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:35:52,929] [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_002689105.1	s__Poseidonia sp002689105	80.6088	237	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002495645.1	s__Poseidonia sp002495645	80.0135	246	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002725275.1	s__Poseidonia sp002725275	78.5672	149	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002714305.1	s__Poseidonia sp002714305	77.866	133	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_002722695.1	s__Poseidonia sp002722695	77.7208	112	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_013330155.1	s__Poseidonia sp8339u	77.6262	106	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.08	98.16	0.89	0.82	3	-
GCA_002502295.1	s__Poseidonia sp002502295	77.3929	126	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625885.1	s__Poseidonia sp902625885	77.2725	97	323	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:35:52,929] [INFO] GTDB search result was written to OceanDNA-a2981/result_gtdb.tsv
[2023-03-16 23:35:52,929] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:35:52,930] [INFO] DFAST_QC result json was written to OceanDNA-a2981/dqc_result.json
[2023-03-16 23:35:52,930] [INFO] DFAST_QC completed!
[2023-03-16 23:35:52,930] [INFO] Total running time: 0h0m40s