[2023-06-05 10:33:27,204] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:27,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:27,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference
[2023-06-05 10:33:28,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:28,506] [INFO] Task started: Prodigal
[2023-06-05 10:33:28,507] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaa68ebd-e7fb-4501-beee-0fa540382954/GCA_934293005.1_ERR7738616_bin.92_genomic.fna.gz | prodigal -d GCA_934293005.1_ERR7738616_bin.92_genomic.fna/cds.fna -a GCA_934293005.1_ERR7738616_bin.92_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:33:45,178] [INFO] Task succeeded: Prodigal
[2023-06-05 10:33:45,178] [INFO] Task started: HMMsearch
[2023-06-05 10:33:45,178] [INFO] Running command: hmmsearch --tblout GCA_934293005.1_ERR7738616_bin.92_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference/reference_markers.hmm GCA_934293005.1_ERR7738616_bin.92_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:33:45,449] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:33:45,451] [INFO] Found 6/6 markers.
[2023-06-05 10:33:45,478] [INFO] Query marker FASTA was written to GCA_934293005.1_ERR7738616_bin.92_genomic.fna/markers.fasta
[2023-06-05 10:33:45,478] [INFO] Task started: Blastn
[2023-06-05 10:33:45,478] [INFO] Running command: blastn -query GCA_934293005.1_ERR7738616_bin.92_genomic.fna/markers.fasta -db /var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference/reference_markers.fasta -out GCA_934293005.1_ERR7738616_bin.92_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:33:46,097] [INFO] Task succeeded: Blastn
[2023-06-05 10:33:46,103] [INFO] Selected 27 target genomes.
[2023-06-05 10:33:46,103] [INFO] Target genome list was writen to GCA_934293005.1_ERR7738616_bin.92_genomic.fna/target_genomes.txt
[2023-06-05 10:33:46,109] [INFO] Task started: fastANI
[2023-06-05 10:33:46,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa68ebd-e7fb-4501-beee-0fa540382954/GCA_934293005.1_ERR7738616_bin.92_genomic.fna.gz --refList GCA_934293005.1_ERR7738616_bin.92_genomic.fna/target_genomes.txt --output GCA_934293005.1_ERR7738616_bin.92_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:34:00,773] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:00,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:34:00,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:34:00,780] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:34:00,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:34:00,780] [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
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.5387	50	817	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:34:00,783] [INFO] DFAST Taxonomy check result was written to GCA_934293005.1_ERR7738616_bin.92_genomic.fna/tc_result.tsv
[2023-06-05 10:34:00,783] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:34:00,783] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:34:00,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference/checkm_data
[2023-06-05 10:34:00,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:34:00,816] [INFO] Task started: CheckM
[2023-06-05 10:34:00,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934293005.1_ERR7738616_bin.92_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934293005.1_ERR7738616_bin.92_genomic.fna/checkm_input GCA_934293005.1_ERR7738616_bin.92_genomic.fna/checkm_result
[2023-06-05 10:34:51,301] [INFO] Task succeeded: CheckM
[2023-06-05 10:34:51,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:34:51,336] [INFO] ===== Completeness check finished =====
[2023-06-05 10:34:51,336] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:34:51,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934293005.1_ERR7738616_bin.92_genomic.fna/markers.fasta)
[2023-06-05 10:34:51,337] [INFO] Task started: Blastn
[2023-06-05 10:34:51,337] [INFO] Running command: blastn -query GCA_934293005.1_ERR7738616_bin.92_genomic.fna/markers.fasta -db /var/lib/cwl/stg54fd0ba7-687c-4e26-a957-915b5eb33e98/dqc_reference/reference_markers_gtdb.fasta -out GCA_934293005.1_ERR7738616_bin.92_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:52,159] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:52,165] [INFO] Selected 21 target genomes.
[2023-06-05 10:34:52,165] [INFO] Target genome list was writen to GCA_934293005.1_ERR7738616_bin.92_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:34:52,174] [INFO] Task started: fastANI
[2023-06-05 10:34:52,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa68ebd-e7fb-4501-beee-0fa540382954/GCA_934293005.1_ERR7738616_bin.92_genomic.fna.gz --refList GCA_934293005.1_ERR7738616_bin.92_genomic.fna/target_genomes_gtdb.txt --output GCA_934293005.1_ERR7738616_bin.92_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:35:01,090] [INFO] Task succeeded: fastANI
[2023-06-05 10:35:01,108] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 10:35:01,108] [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_016302435.1	s__UBA4334 sp016302435	78.3045	197	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009177185.1	s__UBA4334 sp009177185	77.8041	111	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318775.1	s__UBA4334 sp900318775	77.6541	134	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.63	98.03	0.91	0.87	6	-
GCA_902768125.1	s__UBA4334 sp902768125	77.634	131	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_902786925.1	s__UBA4334 sp902786925	77.5499	141	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483605.1	s__UBA4334 sp017483605	77.5492	144	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.79	96.79	0.77	0.77	2	-
GCA_017614895.1	s__UBA4334 sp017614895	77.4983	108	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316505.1	s__UBA4334 sp900316505	77.4636	150	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.14	0.89	0.83	54	-
GCA_905235525.1	s__UBA4334 sp905235525	77.4502	124	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.02	99.02	0.89	0.89	2	-
GCA_900316975.1	s__UBA4334 sp900316975	77.4406	146	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.29	0.86	0.80	13	-
GCA_017651245.1	s__UBA4334 sp017651245	77.3914	139	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002393555.1	s__UBA4334 sp002393555	77.3397	130	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.14	96.87	0.79	0.76	3	-
GCA_016280445.1	s__UBA4334 sp016280445	77.2409	149	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789725.1	s__UBA4334 sp002363115	77.183	143	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.06	99.06	0.84	0.84	2	-
GCA_017470525.1	s__UBA4334 sp017470525	77.1409	133	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017448825.1	s__UBA4334 sp017448825	77.0285	121	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617805.1	s__UBA4334 sp017617805	76.9647	95	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234125.1	s__UBA4334 sp905234125	76.8682	115	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.16	98.16	0.81	0.81	2	-
GCA_017534815.1	s__UBA4334 sp017534815	76.798	104	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:35:01,111] [INFO] GTDB search result was written to GCA_934293005.1_ERR7738616_bin.92_genomic.fna/result_gtdb.tsv
[2023-06-05 10:35:01,111] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:35:01,115] [INFO] DFAST_QC result json was written to GCA_934293005.1_ERR7738616_bin.92_genomic.fna/dqc_result.json
[2023-06-05 10:35:01,115] [INFO] DFAST_QC completed!
[2023-06-05 10:35:01,115] [INFO] Total running time: 0h1m34s