[2023-06-28 11:10:31,660] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:10:31,664] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:10:31,664] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference
[2023-06-28 11:10:32,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:10:32,932] [INFO] Task started: Prodigal
[2023-06-28 11:10:32,932] [INFO] Running command: gunzip -c /var/lib/cwl/stge7b4a9be-856e-4c71-b5de-52471d060a31/GCA_944321815.1_BRZ_B_bin61_genomic.fna.gz | prodigal -d GCA_944321815.1_BRZ_B_bin61_genomic.fna/cds.fna -a GCA_944321815.1_BRZ_B_bin61_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:10:49,659] [INFO] Task succeeded: Prodigal
[2023-06-28 11:10:49,660] [INFO] Task started: HMMsearch
[2023-06-28 11:10:49,660] [INFO] Running command: hmmsearch --tblout GCA_944321815.1_BRZ_B_bin61_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference/reference_markers.hmm GCA_944321815.1_BRZ_B_bin61_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:10:49,926] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:10:49,928] [INFO] Found 6/6 markers.
[2023-06-28 11:10:49,961] [INFO] Query marker FASTA was written to GCA_944321815.1_BRZ_B_bin61_genomic.fna/markers.fasta
[2023-06-28 11:10:49,961] [INFO] Task started: Blastn
[2023-06-28 11:10:49,962] [INFO] Running command: blastn -query GCA_944321815.1_BRZ_B_bin61_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference/reference_markers.fasta -out GCA_944321815.1_BRZ_B_bin61_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:10:50,580] [INFO] Task succeeded: Blastn
[2023-06-28 11:10:50,585] [INFO] Selected 27 target genomes.
[2023-06-28 11:10:50,586] [INFO] Target genome list was writen to GCA_944321815.1_BRZ_B_bin61_genomic.fna/target_genomes.txt
[2023-06-28 11:10:50,588] [INFO] Task started: fastANI
[2023-06-28 11:10:50,588] [INFO] Running command: fastANI --query /var/lib/cwl/stge7b4a9be-856e-4c71-b5de-52471d060a31/GCA_944321815.1_BRZ_B_bin61_genomic.fna.gz --refList GCA_944321815.1_BRZ_B_bin61_genomic.fna/target_genomes.txt --output GCA_944321815.1_BRZ_B_bin61_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:11:07,532] [INFO] Task succeeded: fastANI
[2023-06-28 11:11:07,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:11:07,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:11:07,548] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:11:07,549] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:11:07,549] [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
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.1127	61	970	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	77.0162	66	970	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	77.0066	66	970	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	76.8378	59	970	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	76.8039	57	970	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	76.7739	76	970	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	76.4842	57	970	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:11:07,551] [INFO] DFAST Taxonomy check result was written to GCA_944321815.1_BRZ_B_bin61_genomic.fna/tc_result.tsv
[2023-06-28 11:11:07,552] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:11:07,553] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:11:07,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference/checkm_data
[2023-06-28 11:11:07,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:11:07,588] [INFO] Task started: CheckM
[2023-06-28 11:11:07,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321815.1_BRZ_B_bin61_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321815.1_BRZ_B_bin61_genomic.fna/checkm_input GCA_944321815.1_BRZ_B_bin61_genomic.fna/checkm_result
[2023-06-28 11:11:57,520] [INFO] Task succeeded: CheckM
[2023-06-28 11:11:57,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:11:57,545] [INFO] ===== Completeness check finished =====
[2023-06-28 11:11:57,545] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:11:57,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321815.1_BRZ_B_bin61_genomic.fna/markers.fasta)
[2023-06-28 11:11:57,546] [INFO] Task started: Blastn
[2023-06-28 11:11:57,546] [INFO] Running command: blastn -query GCA_944321815.1_BRZ_B_bin61_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9023cec-2edc-4f9f-836c-2c91c9d02d6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321815.1_BRZ_B_bin61_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:11:58,419] [INFO] Task succeeded: Blastn
[2023-06-28 11:11:58,424] [INFO] Selected 20 target genomes.
[2023-06-28 11:11:58,425] [INFO] Target genome list was writen to GCA_944321815.1_BRZ_B_bin61_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:11:58,443] [INFO] Task started: fastANI
[2023-06-28 11:11:58,444] [INFO] Running command: fastANI --query /var/lib/cwl/stge7b4a9be-856e-4c71-b5de-52471d060a31/GCA_944321815.1_BRZ_B_bin61_genomic.fna.gz --refList GCA_944321815.1_BRZ_B_bin61_genomic.fna/target_genomes_gtdb.txt --output GCA_944321815.1_BRZ_B_bin61_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:12:07,664] [INFO] Task succeeded: fastANI
[2023-06-28 11:12:07,680] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:12:07,680] [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_900544305.1	s__Limisoma sp900544305	97.9547	842	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	97.92	97.84	0.88	0.86	3	conclusive
GCA_900548875.1	s__Limisoma sp900548875	88.837	771	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	97.13	97.13	0.85	0.85	2	-
GCA_900541935.1	s__Limisoma sp900541935	77.6267	95	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.32	96.63	0.93	0.87	3	-
GCA_017694955.1	s__Limisoma faecipullorum	77.6233	121	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437795.1	s__Limisoma sp000437795	77.3791	160	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.05	97.80	0.87	0.76	12	-
GCA_004555955.1	s__Limisoma sp004555955	76.8308	119	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550025.1	s__Limisoma gallistercoris	76.8255	126	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.17	98.10	0.82	0.79	4	-
GCA_900541555.1	s__Limisoma intestinavium	76.7744	97	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.58	98.56	0.93	0.91	3	-
GCA_910586915.1	s__Bacteroides sp910586915	76.4716	55	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905207705.1	s__Avimuribaculum sp905207705	76.4691	56	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Avimuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292745.1	s__SFRY01 sp004562065	76.3573	58	970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__SFRY01	95.0	98.75	98.75	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-28 11:12:07,682] [INFO] GTDB search result was written to GCA_944321815.1_BRZ_B_bin61_genomic.fna/result_gtdb.tsv
[2023-06-28 11:12:07,683] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:12:07,686] [INFO] DFAST_QC result json was written to GCA_944321815.1_BRZ_B_bin61_genomic.fna/dqc_result.json
[2023-06-28 11:12:07,686] [INFO] DFAST_QC completed!
[2023-06-28 11:12:07,686] [INFO] Total running time: 0h1m36s