[2023-06-28 13:30:05,051] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:30:05,053] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:30:05,053] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference
[2023-06-28 13:30:06,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:30:06,489] [INFO] Task started: Prodigal
[2023-06-28 13:30:06,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9c0f28c-4fa8-466d-90f8-e4e7b3025956/GCA_944326655.1_E12_bin100_genomic.fna.gz | prodigal -d GCA_944326655.1_E12_bin100_genomic.fna/cds.fna -a GCA_944326655.1_E12_bin100_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:30:09,530] [INFO] Task succeeded: Prodigal
[2023-06-28 13:30:09,531] [INFO] Task started: HMMsearch
[2023-06-28 13:30:09,531] [INFO] Running command: hmmsearch --tblout GCA_944326655.1_E12_bin100_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference/reference_markers.hmm GCA_944326655.1_E12_bin100_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:30:09,805] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:30:09,807] [INFO] Found 6/6 markers.
[2023-06-28 13:30:09,835] [INFO] Query marker FASTA was written to GCA_944326655.1_E12_bin100_genomic.fna/markers.fasta
[2023-06-28 13:30:09,835] [INFO] Task started: Blastn
[2023-06-28 13:30:09,835] [INFO] Running command: blastn -query GCA_944326655.1_E12_bin100_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference/reference_markers.fasta -out GCA_944326655.1_E12_bin100_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:11,235] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:11,240] [INFO] Selected 22 target genomes.
[2023-06-28 13:30:11,241] [INFO] Target genome list was writen to GCA_944326655.1_E12_bin100_genomic.fna/target_genomes.txt
[2023-06-28 13:30:11,319] [INFO] Task started: fastANI
[2023-06-28 13:30:11,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c0f28c-4fa8-466d-90f8-e4e7b3025956/GCA_944326655.1_E12_bin100_genomic.fna.gz --refList GCA_944326655.1_E12_bin100_genomic.fna/target_genomes.txt --output GCA_944326655.1_E12_bin100_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:30:22,101] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:22,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:30:22,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:30:22,104] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:30:22,104] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:30:22,104] [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
--------------------------------------------------------------------------------
[2023-06-28 13:30:22,107] [INFO] DFAST Taxonomy check result was written to GCA_944326655.1_E12_bin100_genomic.fna/tc_result.tsv
[2023-06-28 13:30:22,107] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:30:22,108] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:30:22,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference/checkm_data
[2023-06-28 13:30:22,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:30:22,324] [INFO] Task started: CheckM
[2023-06-28 13:30:22,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944326655.1_E12_bin100_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944326655.1_E12_bin100_genomic.fna/checkm_input GCA_944326655.1_E12_bin100_genomic.fna/checkm_result
[2023-06-28 13:30:40,642] [INFO] Task succeeded: CheckM
[2023-06-28 13:30:40,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.38%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 13:30:40,661] [INFO] ===== Completeness check finished =====
[2023-06-28 13:30:40,661] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:30:40,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944326655.1_E12_bin100_genomic.fna/markers.fasta)
[2023-06-28 13:30:40,662] [INFO] Task started: Blastn
[2023-06-28 13:30:40,662] [INFO] Running command: blastn -query GCA_944326655.1_E12_bin100_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcb653cf-32af-4047-89dd-a1a50db7fba1/dqc_reference/reference_markers_gtdb.fasta -out GCA_944326655.1_E12_bin100_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:41,614] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:41,691] [INFO] Selected 21 target genomes.
[2023-06-28 13:30:41,692] [INFO] Target genome list was writen to GCA_944326655.1_E12_bin100_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:30:41,710] [INFO] Task started: fastANI
[2023-06-28 13:30:41,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c0f28c-4fa8-466d-90f8-e4e7b3025956/GCA_944326655.1_E12_bin100_genomic.fna.gz --refList GCA_944326655.1_E12_bin100_genomic.fna/target_genomes_gtdb.txt --output GCA_944326655.1_E12_bin100_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:30:50,253] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:50,276] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:30:50,276] [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_900551675.1	s__Stercorousia sp900551675	79.5749	248	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_000438175.1	s__Stercorousia faecigallinarum	79.0854	263	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.53	97.95	0.88	0.85	4	-
GCA_905216055.1	s__Stercorousia sp905216055	78.8334	250	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761225.1	s__Stercorousia sp900761225	78.6527	235	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555175.1	s__Stercorousia sp900555175	78.5821	142	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.94	0.94	2	-
GCA_905212085.1	s__Stercorousia sp905212085	78.3635	207	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433095.1	s__Stercorousia sp000433095	78.3414	230	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_000437435.1	s__Stercorousia sp000437435	78.2295	241	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.52	97.52	0.91	0.91	3	-
GCA_900548405.1	s__Stercorousia sp001917115	78.1296	208	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.35	95.50	0.91	0.85	8	-
GCA_900752845.1	s__Stercorousia sp900752845	78.0831	176	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.76	99.76	0.83	0.83	2	-
GCA_910588555.1	s__Stercorousia sp910588555	77.9313	194	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001765415.1	s__Stercorousia sp001765415	77.4333	168	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
GCA_003150395.1	s__Scatenecus sp003150395	77.2349	110	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795965.1	s__Stercorousia sp902795965	77.1569	145	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554385.1	s__Scatousia sp900554385	76.9701	92	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.41	98.83	0.97	0.96	3	-
GCA_902772945.1	s__Stercorousia sp902772945	76.9347	94	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551915.1	s__Scatenecus faecavium	76.8436	113	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	98.79	98.66	0.89	0.87	5	-
GCA_002361485.1	s__UBA2813 sp002361485	76.3236	64	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	97.91	97.91	0.90	0.90	2	-
GCA_900314375.1	s__UBA2813 sp900314375	76.1157	63	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	99.17	98.57	0.90	0.80	5	-
GCA_902801985.1	s__UBA2813 sp902801985	76.0346	50	474	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:30:50,278] [INFO] GTDB search result was written to GCA_944326655.1_E12_bin100_genomic.fna/result_gtdb.tsv
[2023-06-28 13:30:50,279] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:30:50,284] [INFO] DFAST_QC result json was written to GCA_944326655.1_E12_bin100_genomic.fna/dqc_result.json
[2023-06-28 13:30:50,284] [INFO] DFAST_QC completed!
[2023-06-28 13:30:50,284] [INFO] Total running time: 0h0m45s